Index (htsjdk 2.8.1 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Z

A

a - Static variable in class htsjdk.samtools.util.SequenceUtil: Byte typed variables for all normal bases.
A - Static variable in class htsjdk.samtools.util.SequenceUtil: Byte typed variables for all normal bases.
a - Variable in class htsjdk.samtools.util.Tuple
AbstractAsyncWriter<T> - Class in htsjdk.samtools.util: Abstract class that is designed to be extended and specialized to provide an asynchronous wrapper around any kind of Writer class that takes an object and writes it out somehow.
AbstractAsyncWriter(int) - Constructor for class htsjdk.samtools.util.AbstractAsyncWriter: Creates an AbstractAsyncWriter that will use the provided WriterRunnable to consume from the internal queue and write records into the synchronous writer.
AbstractBAMFileIndex - Class in htsjdk.samtools: Provides basic, generic capabilities to be used reading BAM index files.
AbstractBAMFileIndex(SeekableStream, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.AbstractBAMFileIndex
AbstractBAMFileIndex(File, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.AbstractBAMFileIndex
AbstractBAMFileIndex(File, SAMSequenceDictionary, boolean) - Constructor for class htsjdk.samtools.AbstractBAMFileIndex
AbstractBitCodec<T> - Class in htsjdk.samtools.cram.encoding
AbstractBitCodec() - Constructor for class htsjdk.samtools.cram.encoding.AbstractBitCodec
AbstractFeatureCodec<FEATURE_TYPE extends Feature,SOURCE> - Class in htsjdk.tribble: Simple basic class providing much of the basic functionality of codecs Every concrete subclass must implement FeatureCodec.canDecode(String) to indicate whether it can decode the file.
AbstractFeatureCodec(Class<FEATURE_TYPE>) - Constructor for class htsjdk.tribble.AbstractFeatureCodec
AbstractFeatureReader<T extends Feature,SOURCE> - Class in htsjdk.tribble: jrobinso
the feature reader class, which uses indices and codecs to read in Tribble file formats.
AbstractFeatureReader(String, FeatureCodec<T, SOURCE>) - Constructor for class htsjdk.tribble.AbstractFeatureReader
AbstractFeatureReader.ComponentMethods - Class in htsjdk.tribble
AbstractIndex - Class in htsjdk.tribble.index: An abstract implementation of the index class.
AbstractIndex() - Constructor for class htsjdk.tribble.index.AbstractIndex: create an abstract index, with defaults for the version value, and empty properties and chromosome lists
AbstractIndex(String) - Constructor for class htsjdk.tribble.index.AbstractIndex: create an index file from the target feature file
AbstractIndex(File) - Constructor for class htsjdk.tribble.index.AbstractIndex
AbstractIndex(AbstractIndex) - Constructor for class htsjdk.tribble.index.AbstractIndex
AbstractIndex.BlockStats - Class in htsjdk.tribble.index
AbstractIndex.IndexType - Enum in htsjdk.tribble.index
AbstractIterator<E> - Class in htsjdk.samtools.util: Base class of implementing iterators.
AbstractIterator() - Constructor for class htsjdk.samtools.util.AbstractIterator
AbstractJavascriptFilter<HEADER,TYPE> - Class in htsjdk.samtools.filter: Javascript filter with HEADER type containing TYPE records.
AbstractJavascriptFilter(File, HEADER) - Constructor for class htsjdk.samtools.filter.AbstractJavascriptFilter: constructor using a java.io.File script, compiles the script, puts 'header' in the bindings
AbstractJavascriptFilter(String, HEADER) - Constructor for class htsjdk.samtools.filter.AbstractJavascriptFilter: constructor using a java.lang.String script, compiles the script, puts 'header' in the bindings
AbstractJavascriptFilter(Reader, HEADER) - Constructor for class htsjdk.samtools.filter.AbstractJavascriptFilter: Constructor, compiles script, put header in the bindings
AbstractLocusInfo<E extends AbstractRecordAndOffset> - Class in htsjdk.samtools.util: The unit of iteration for AbstractLocusIterator.
AbstractLocusInfo(SAMSequenceRecord, int) - Constructor for class htsjdk.samtools.util.AbstractLocusInfo
AbstractLocusIterator<T extends AbstractRecordAndOffset,K extends AbstractLocusInfo<T>> - Class in htsjdk.samtools.util: Iterator that traverses a SAM File, accumulating information on a per-locus basis.
AbstractLocusIterator(SamReader, IntervalList, boolean) - Constructor for class htsjdk.samtools.util.AbstractLocusIterator: Prepare to iterate through the given SAM records, skipping non-primary alignments
AbstractProgressLogger - Class in htsjdk.samtools.util: Abstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.
AbstractProgressLogger(String, String, int) - Constructor for class htsjdk.samtools.util.AbstractProgressLogger: Construct an AbstractProgressLogger.
AbstractReader - Class in htsjdk.samtools.cram.encoding.reader
AbstractReader() - Constructor for class htsjdk.samtools.cram.encoding.reader.AbstractReader
AbstractRecordAndOffset - Class in htsjdk.samtools.util: Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality at the genomic position described the containing AbstractLocusInfo.
AbstractRecordAndOffset(SAMRecord, int, int, int) - Constructor for class htsjdk.samtools.util.AbstractRecordAndOffset
AbstractRecordAndOffset(SAMRecord, int) - Constructor for class htsjdk.samtools.util.AbstractRecordAndOffset
AbstractSAMHeaderRecord - Class in htsjdk.samtools: Base class for the various concrete records in a SAM header, providing uniform access to the attributes.
AbstractSAMHeaderRecord() - Constructor for class htsjdk.samtools.AbstractSAMHeaderRecord
AbstractVCFCodec - Class in htsjdk.variant.vcf
AbstractVCFCodec() - Constructor for class htsjdk.variant.vcf.AbstractVCFCodec
abuts(QueryInterval) - Method in class htsjdk.samtools.QueryInterval
abuts(Interval) - Method in class htsjdk.samtools.util.Interval: Returns true if this interval overlaps the other interval, otherwise false.
accept(TYPE) - Method in class htsjdk.samtools.filter.AbstractJavascriptFilter: Evaluates this predicate on the given argument
ACCEPTABLE_VERSIONS - Static variable in class htsjdk.samtools.SAMFileHeader
acceptableAlleleBases(String) - Static method in class htsjdk.variant.variantcontext.Allele
acceptableAlleleBases(String, boolean) - Static method in class htsjdk.variant.variantcontext.Allele
acceptableAlleleBases(byte[]) - Static method in class htsjdk.variant.variantcontext.Allele
acceptableAlleleBases(byte[], boolean) - Static method in class htsjdk.variant.variantcontext.Allele
Accessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.Accessor
AD(int[]) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder: This genotype has this AD value
ADAccessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.ADAccessor
add(BAMFileSpan) - Method in class htsjdk.samtools.BAMFileSpan: Merge one span into another
add(Chunk) - Method in class htsjdk.samtools.BAMFileSpan: Adds a new chunk to this list.
add(CigarElement) - Method in class htsjdk.samtools.Cigar
add(CramCompressionRecord) - Method in class htsjdk.samtools.cram.digest.ContentDigests
add(int, int, int) - Method in class htsjdk.samtools.cram.structure.AlignmentSpan: Add multiple reads to the span.
add(SAMRecord) - Method in class htsjdk.samtools.DuplicateSet: Adds a record to the set and returns zero if either the set is empty, or it is a duplicate of the records already in the set.
add(FastaSequenceIndexEntry) - Method in class htsjdk.samtools.reference.FastaSequenceIndex: Add a new index entry to the list.
add(E) - Method in class htsjdk.samtools.util.AbstractLocusInfo: Accumulates info for one read aligned to the locus.
add(E) - Method in class htsjdk.samtools.util.DiskBackedQueue: Add the record to the tail of the queue, spilling to disk if necessary Must check that (canAdd() == true) before calling this method
add(Interval) - Method in class htsjdk.samtools.util.IntervalList: Adds an interval to the list of intervals.
add(K, V) - Method in class htsjdk.samtools.util.ListMap: Adds a single value to the list stored under a key.
add(long, FastqReader...) - Method in class htsjdk.samtools.util.QualityEncodingDetector: Adds the provided reader's records to the detector.
add(long, SamReader) - Method in class htsjdk.samtools.util.QualityEncodingDetector: Adds the provided reader's records to the detector.
add(long, CloseableIterator<SAMRecord>, boolean) - Method in class htsjdk.samtools.util.QualityEncodingDetector: Adds the provided iterator's records (optionally using the original qualities) to the detector.
add(long, CloseableIterator<SAMRecord>) - Method in class htsjdk.samtools.util.QualityEncodingDetector
add(FastqRecord) - Method in class htsjdk.samtools.util.QualityEncodingDetector: Adds the provided record's qualities to the detector.
add(SAMRecord, boolean) - Method in class htsjdk.samtools.util.QualityEncodingDetector: Adds the provided record's qualities to the detector.
add(SAMRecord) - Method in class htsjdk.samtools.util.QualityEncodingDetector
add(SamRecordWithOrdinal) - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer: Add the given SAMRecordIndex to the buffer.
add(T) - Method in class htsjdk.samtools.util.SortingCollection
add(long) - Method in class htsjdk.samtools.util.SortingLongCollection: Add a value to the collection.
add(Genotype) - Method in class htsjdk.variant.variantcontext.GenotypesContext: Adds a single genotype to this context.
add(int, Genotype) - Method in class htsjdk.variant.variantcontext.GenotypesContext
add(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
add(VariantContext) - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter
addAlignment(SAMRecord) - Method in interface htsjdk.samtools.SAMFileWriter
addAlignment(SAMRecord) - Method in class htsjdk.samtools.SAMFileWriterImpl: Add an alignment record to be emitted by the writer.
addAll(Collection<? extends E>) - Method in class htsjdk.samtools.util.DiskBackedQueue: Add all elements from collection c to this DiskBackedQueue Must check that (canAdd() == true) before calling this method
addall(Collection<Interval>) - Method in class htsjdk.samtools.util.IntervalList: Adds a Collection of intervals to the list of intervals.
addAll(List<T>, List<? extends Locatable>) - Method in class htsjdk.samtools.util.OverlapDetector: Adds all items to the overlap detector.
addAll(Collection<? extends Genotype>) - Method in class htsjdk.variant.variantcontext.GenotypesContext: Adds all of the genotypes to this context See GenotypesContext.add(Genotype) for important information about this functions constraints and performance costs
addAll(int, Collection<? extends Genotype>) - Method in class htsjdk.variant.variantcontext.GenotypesContext
addAllMetrics(Iterable<BEAN>) - Method in class htsjdk.samtools.metrics.MetricsFile: Add multiple metric beans at once.
addComment(String) - Method in class htsjdk.samtools.SAMFileHeader
addCoverage(int, int) - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
addCramRecords(Iterable<CramCompressionRecord>) - Method in class htsjdk.samtools.cram.digest.ContentDigests
addDeleted(SAMRecord, int) - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo: Accumulate info for one read with a deletion
addEntry(CRAIEntry) - Method in class htsjdk.samtools.cram.CRAIIndex: Add a single entry to the CRAI index.
addEntry(CRAIEntry) - Method in class htsjdk.samtools.CRAMCRAIIndexer
addExon(FullBEDFeature.Exon) - Method in class htsjdk.tribble.bed.FullBEDFeature
addExon(int, int, int, int, int) - Method in class htsjdk.tribble.bed.FullBEDFeature
addFeature(Feature, long) - Method in class htsjdk.tribble.index.DynamicIndexCreator
addFeature(Feature, long) - Method in interface htsjdk.tribble.index.IndexCreator: Add a feature to the index
addFeature(Feature, long) - Method in class htsjdk.tribble.index.interval.IntervalIndexCreator
addFeature(Feature, long) - Method in class htsjdk.tribble.index.linear.LinearIndexCreator: add a feature to the index
addFeature(Feature, long) - Method in class htsjdk.tribble.index.tabix.TabixIndexCreator
addFilter(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
addFilters(Collection<String>) - Method in class htsjdk.variant.variantcontext.CommonInfo
addFrag(String, int, int, boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a skeletal fragment (non-PE) record to the set using the provided contig start and strand information.
addFrag(String, int, int, boolean, boolean, String, String, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
addFrag(String, int, int, boolean, boolean, String, String, int, boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
addFrag(String, int, int, boolean, boolean, String, String, int, boolean, boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
addGenotype(BCF2Encoder, VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.FTGenotypesWriter
addGenotype(BCF2Encoder, VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
addGenotype(BCF2Encoder, VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GTWriter
addGenotype(BCF2Encoder, VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
addGenotypeData(VariantContext, Map<Allele, String>, List<String>, StringBuilder) - Method in class htsjdk.variant.vcf.VCFEncoder
addHeader(Header) - Method in class htsjdk.samtools.metrics.MetricsFile: Adds a header to the collection of metrics.
addHistogram(Histogram<HKEY>) - Method in class htsjdk.samtools.metrics.MetricsFile: Adds a histogram to the list of histograms in the metrics file.
addHistogram(Histogram<K>) - Method in class htsjdk.samtools.util.Histogram: Mutable method that allows the addition of a Histogram into the current one.
addInitialChunk(Chunk) - Method in class htsjdk.samtools.Bin: Adds the first chunk to the bin
addInserted(SAMRecord, int) - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo: Accumulate info for one read with an insertion.
addLhs(T, Locatable) - Method in class htsjdk.samtools.util.OverlapDetector: Adds a Locatable to the set of Locatables against which to match candidates.
addMetaDataLine(VCFHeaderLine) - Method in class htsjdk.variant.vcf.VCFHeader: Adds a new line to the VCFHeader.
addMetric(BEAN) - Method in class htsjdk.samtools.metrics.MetricsFile: Adds a bean to the collection of metrics.
addMismatches(int, int) - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
addPair(String, int, int, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a skeletal pair of records to the set using the provided contig starts.
addPair(String, int, int, int, boolean, boolean, String, String, boolean, boolean, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
addPair(String, int, int, int, int, boolean, boolean, String, String, boolean, boolean, boolean, boolean, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
addPair(String, int, int, int, boolean, boolean, String, String, boolean, boolean, boolean, boolean, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
addProgramRecord(SAMProgramRecord) - Method in class htsjdk.samtools.SAMFileHeader
addProperties(Map<String, String>) - Method in class htsjdk.tribble.index.AbstractIndex
addProperties(Map<String, String>) - Method in interface htsjdk.tribble.index.MutableIndex
addProperty(String, String) - Method in class htsjdk.tribble.index.AbstractIndex
addProperty(String, String) - Method in class htsjdk.tribble.index.DynamicIndexCreator
addProperty(String, String) - Method in interface htsjdk.tribble.index.MutableIndex
addProperty(String, String) - Method in class htsjdk.tribble.index.TribbleIndexCreator
addQualityScores(SAMRecord, CramCompressionRecord, ReferenceTracks) - Method in class htsjdk.samtools.cram.lossy.QualityScorePreservation
addReadGroup(SAMReadGroupRecord) - Method in class htsjdk.samtools.SAMFileHeader
addRecord(SAMRecord) - Method in class htsjdk.samtools.SAMRecordSetBuilder: The record should already have the DS and MC tags computed
addSAMRecords(Iterable<SAMRecord>) - Method in class htsjdk.samtools.cram.digest.ContentDigests
addSequence(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMFileHeader
addSequence(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMSequenceDictionary
addSequenceAlias(String, String) - Method in class htsjdk.samtools.SAMSequenceDictionary: Add an alias to a SAMSequenceRecord.
addSingle(int, int) - Method in class htsjdk.samtools.cram.structure.AlignmentSpan: Add a single read to the span
addSoftClippedBasesToEndsOfCigar(Cigar, boolean, int, int) - Static method in class htsjdk.samtools.util.CigarUtil: Adds additional soft-clipped bases at the 3' and/or 5' end of the cigar.
addStandardFormatLines(Set<VCFHeaderLine>, boolean, Collection<String>) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines: Adds header lines for each of the format fields in IDs to header, returning the set of IDs without standard descriptions, unless throwErrorForMissing is true, in which case this situation results in a TribbleException
addStandardFormatLines(Set<VCFHeaderLine>, boolean, String...) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
addStandardInfoLines(Set<VCFHeaderLine>, boolean, Collection<String>) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines: Adds header lines for each of the info fields in IDs to header, returning the set of IDs without standard descriptions, unless throwErrorForMissing is true, in which case this situation results in a TribbleException.
addStandardInfoLines(Set<VCFHeaderLine>, boolean, String...) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
addUnmappedFragment(String) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds an unmapped fragment read to the builder.
addUnmappedPair(String) - Method in class htsjdk.samtools.SAMRecordSetBuilder: Adds a pair with both ends unmapped to the builder.
addValidationError(SAMValidationError) - Method in class htsjdk.samtools.SAMFileHeader
advance() - Method in class htsjdk.samtools.NotPrimarySkippingIterator
advance() - Method in class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
advance() - Method in class htsjdk.samtools.util.AbstractIterator
advance() - Method in class htsjdk.tribble.readers.LineIteratorImpl
advanceToAlignmentInContainer(int, int) - Method in class htsjdk.samtools.CRAMIterator: Skip cached records until given alignment start position.
after(Date) - Method in class htsjdk.samtools.util.RelativeIso8601Date
AggregateFilter - Class in htsjdk.samtools.filter: Aggregates multiple filters and provides a method for applying them all to a given record with one method call.
AggregateFilter(List<SamRecordFilter>) - Constructor for class htsjdk.samtools.filter.AggregateFilter: Constructor
AlignedFilter - Class in htsjdk.samtools.filter: Filter to either include or exclude aligned reads $Id$
AlignedFilter(boolean) - Constructor for class htsjdk.samtools.filter.AlignedFilter
AlignmentBlock - Class in htsjdk.samtools: Represents the contiguous alignment of a subset of read bases to a reference sequence.
alignmentDelta - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
alignmentSpan - Variable in class htsjdk.samtools.cram.CRAIEntry
AlignmentSpan - Class in htsjdk.samtools.cram.structure: A span of reads on a single reference.
AlignmentSpan(int, int) - Constructor for class htsjdk.samtools.cram.structure.AlignmentSpan: Create a new span with a single read in it.
AlignmentSpan(int, int, int) - Constructor for class htsjdk.samtools.cram.structure.AlignmentSpan: Create a new span with a multiple reads in it.
alignmentSpan - Variable in class htsjdk.samtools.cram.structure.Container
alignmentSpan - Variable in class htsjdk.samtools.cram.structure.Slice
alignmentStart - Variable in class htsjdk.samtools.cram.CRAIEntry
alignmentStart - Variable in class htsjdk.samtools.cram.structure.Container
alignmentStart - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
alignmentStart - Variable in class htsjdk.samtools.cram.structure.Slice
alignmentStartCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
ALL - Static variable in class htsjdk.samtools.cram.digest.ContentDigests
all() - Static method in class htsjdk.samtools.cram.lossy.ReadCategory
ALL_BYTES_USED - Static variable in class htsjdk.samtools.cram.build.CompressionHeaderFactory
allDefaults() - Static method in class htsjdk.samtools.Defaults: Returns a map of all default values (keys are names), lexicographically sorted by keys.
Allele - Class in htsjdk.variant.variantcontext: Immutable representation of an allele.
Allele(byte[], boolean) - Constructor for class htsjdk.variant.variantcontext.Allele
Allele(String, boolean) - Constructor for class htsjdk.variant.variantcontext.Allele
Allele(Allele, boolean) - Constructor for class htsjdk.variant.variantcontext.Allele: Creates a new allele based on the provided one.
ALLELE_COUNT_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
ALLELE_FREQUENCY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
ALLELE_NUMBER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
alleleIndex1 - Variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
alleleIndex2 - Variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
alleleMap - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
alleles(List<Allele>) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder: Set this genotype's alleles
alleles - Variable in class htsjdk.variant.variantcontext.VariantContext: A set of the alleles segregating in this context
alleles(Collection<Allele>) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder: Tells this builder to use this collection of alleles for the resulting VariantContext
alleles(List<String>) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
alleles(String...) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
ALLOW_UNBOUND_DESCRIPTIONS - Static variable in class htsjdk.variant.vcf.VCFHeaderLine
allowFlagValues - Variable in enum htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType
alStartC - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
ALT_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
AM - Variable in class htsjdk.samtools.SAMTagUtil
ANCESTRAL_ALLELE_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
anyploidPloidyToPLIndexToAlleleIndices - Static variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods: A cache of PL index to a list of alleles for any ploidy.
AP_delta - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
APDelta - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
APDelta - Variable in class htsjdk.samtools.cram.structure.CompressionHeader
append(K, V) - Method in class htsjdk.samtools.util.CollectionUtil.MultiMap
appendAll(K, Collection<? extends V>) - Method in class htsjdk.samtools.util.CollectionUtil.MultiMap
appendToPath(String, String) - Static method in class htsjdk.tribble.util.ParsingUtils: Add the indexExtension to the filepath, preserving query string elements if present.
areHeadersEqual(MetricsFile) - Method in class htsjdk.samtools.metrics.MetricsFile
areHistogramsEqual(MetricsFile) - Method in class htsjdk.samtools.metrics.MetricsFile
areInSameOrAdjacentBlocks(long, long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
areMetricsAndHistogramsEqual(File, File) - Static method in class htsjdk.samtools.metrics.MetricsFile: Compare the metrics and histograms in two files, ignoring headers.
areMetricsEqual(MetricsFile) - Method in class htsjdk.samtools.metrics.MetricsFile
areMetricsEqual(File, File) - Static method in class htsjdk.samtools.metrics.MetricsFile: Compare the metrics in two files, ignoring headers and histograms.
areReferenceTracksRequired() - Method in class htsjdk.samtools.cram.lossy.QualityScorePreservation
areSequenceDictionariesEqual(SAMSequenceDictionary, SAMSequenceDictionary) - Static method in class htsjdk.samtools.util.SequenceUtil: Returns true if both parameters are null or equal, otherwise returns false
array(InputStream) - Static method in class htsjdk.samtools.cram.io.CramArray: Read CRAM int array from a InputStream.
arrayMax(double[]) - Static method in class htsjdk.variant.utils.GeneralUtils
AS - Variable in class htsjdk.samtools.SAMTagUtil
asBaiSeekableStreamOrNull(SeekableStream, SAMSequenceDictionary) - Static method in enum htsjdk.samtools.SamIndexes
asBaiStreamOrNull(InputStream, SAMSequenceDictionary) - Static method in enum htsjdk.samtools.SamIndexes
AsciiFeatureCodec<T extends Feature> - Class in htsjdk.tribble: A convenience base class for codecs that want to read in features from ASCII lines.
AsciiFeatureCodec(Class<T>) - Constructor for class htsjdk.tribble.AsciiFeatureCodec
AsciiLineReader - Class in htsjdk.tribble.readers: A simple class that provides AsciiLineReader.readLine() functionality around a PositionalBufferedStream BufferedReader and its BufferedReader.readLine() method should be used in preference to this class (when the LocationAware functionality is not required) because it offers greater performance.
AsciiLineReader(InputStream) - Constructor for class htsjdk.tribble.readers.AsciiLineReader
AsciiLineReader(PositionalBufferedStream) - Constructor for class htsjdk.tribble.readers.AsciiLineReader
AsciiLineReaderIterator - Class in htsjdk.tribble.readers: A class that iterates over the lines and line positions in an AsciiLineReader.
AsciiLineReaderIterator(AsciiLineReader) - Constructor for class htsjdk.tribble.readers.AsciiLineReaderIterator
AsciiWriter - Class in htsjdk.samtools.util: Fast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion.
AsciiWriter(OutputStream) - Constructor for class htsjdk.samtools.util.AsciiWriter
asEmptyIfNull(Object) - Static method in class htsjdk.samtools.util.StringUtil
ASSEMBLY_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
assertCharactersNotInString(String, char...) - Static method in class htsjdk.samtools.util.StringUtil: Checks that a String doesn't contain one or more characters of interest.
assertDirectoryIsReadable(File) - Static method in class htsjdk.samtools.util.IOUtil: Checks that a directory is non-null, extent, readable and a directory otherwise a runtime exception is thrown.
assertDirectoryIsWritable(File) - Static method in class htsjdk.samtools.util.IOUtil: Checks that a directory is non-null, extent, writable and a directory otherwise a runtime exception is thrown.
assertFileIsReadable(File) - Static method in class htsjdk.samtools.util.IOUtil: Checks that a file is non-null, exists, is not a directory and is readable.
assertFileIsReadable(Path) - Static method in class htsjdk.samtools.util.IOUtil: Checks that a file is non-null, exists, is not a directory and is readable.
assertFileIsWritable(File) - Static method in class htsjdk.samtools.util.IOUtil: Checks that a file is non-null, and is either extent and writable, or non-existent but that the parent directory exists and is writable.
assertFilesAreReadable(List<File>) - Static method in class htsjdk.samtools.util.IOUtil: Checks that each file is non-null, exists, is not a directory and is readable.
assertFilesAreWritable(List<File>) - Static method in class htsjdk.samtools.util.IOUtil: Checks that each file is non-null, and is either extent and writable, or non-existent but that the parent directory exists and is writable.
assertFilesEqual(File, File) - Static method in class htsjdk.samtools.util.IOUtil: Checks that the two files are the same length, and have the same content, otherwise throws a runtime exception.
assertFileSizeNonZero(File) - Static method in class htsjdk.samtools.util.IOUtil: Checks that a file is of non-zero length
AssertingIterator(CloseableIterator<SAMRecord>) - Constructor for class htsjdk.samtools.SamReader.AssertingIterator
assertInputIsValid(String) - Static method in class htsjdk.samtools.util.IOUtil: Checks that an input is is non-null, a URL or a file, exists, and if its a file then it is not a directory and is readable.
assertInputsAreValid(List<String>) - Static method in class htsjdk.samtools.util.IOUtil: Checks that each string is non-null, exists or is a URL, and if it is a file then not a directory and is readable.
assertMate(SAMRecord, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil
assertNonDefectiveFile(File) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
assertOrderedNonOverlapping(Iterator<Interval>, SAMSequenceDictionary) - Static method in class htsjdk.samtools.util.IntervalUtil: Throws RuntimeException if the given intervals are not locus ordered and non-overlapping
assertPairValid(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMTestUtil: Basic sanity check for a pair of SAMRecords.
assertReadValid(SAMRecord) - Method in class htsjdk.samtools.SAMTestUtil: Basic sanity check for a SAMRecord.
assertSameDictionary(SAMSequenceDictionary) - Method in class htsjdk.samtools.SAMSequenceDictionary: Non-comprehensive SAMSequenceDictionary.equals(Object)-assertion: instead of calling SAMSequenceRecord.equals(Object) on constituent SAMSequenceRecords in this dictionary against its pair in the target dictionary, in order, call SAMSequenceRecord.isSameSequence(SAMSequenceRecord).
assertSequenceDictionariesEqual(SAMSequenceDictionary, SAMSequenceDictionary) - Static method in class htsjdk.samtools.util.SequenceUtil: Throws an exception if both parameters are non-null and unequal.
assertSequenceDictionariesEqual(SAMSequenceDictionary, SAMSequenceDictionary, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil: Throws an exception if both (first) parameters are non-null and unequal (if checkPrefixOnly, checks prefix of lists only).
assertSequenceDictionariesEqual(SAMSequenceDictionary, SAMSequenceDictionary, File, File) - Static method in class htsjdk.samtools.util.SequenceUtil: Throws an exception if both parameters are non-null and unequal, including the filenames.
assertSequenceListsEqual(List<SAMSequenceRecord>, List<SAMSequenceRecord>) - Static method in class htsjdk.samtools.util.SequenceUtil: default signature that forces the lists to be the same size
assertSequenceListsEqual(List<SAMSequenceRecord>, List<SAMSequenceRecord>, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil: Throws an exception only if both (first) parameters are not null optionally check that one list is a (nonempty) prefix of the other.
assertSorted(SAMFileHeader.SortOrder) - Method in class htsjdk.samtools.CRAMIterator
assertSorted(SAMFileHeader.SortOrder) - Method in class htsjdk.samtools.SamReader.AssertingIterator
assertSorted(SAMFileHeader.SortOrder) - Method in interface htsjdk.samtools.SAMRecordIterator: Establishes that records returned by this iterator are expected to be in the specified sort order.
assertSorted(SAMFileHeader.SortOrder) - Method in class htsjdk.samtools.SRAIterator
asString(long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
AsyncBufferedIterator<T> - Class in htsjdk.samtools.util: Iterator that uses a dedicated background thread to perform read-ahead to improve throughput at the expense of increased latency.
AsyncBufferedIterator(Iterator<T>, int) - Constructor for class htsjdk.samtools.util.AsyncBufferedIterator: Creates a new iterator that traverses the given iterator on a background thread
AsyncBufferedIterator(Iterator<T>, int, int) - Constructor for class htsjdk.samtools.util.AsyncBufferedIterator: Creates a new iterator that traverses the given iterator on a background thread
AsyncBufferedIterator(Iterator<T>, int, int, String) - Constructor for class htsjdk.samtools.util.AsyncBufferedIterator: Creates a new iterator that traverses the given iterator on a background thread
AsyncFastqWriter - Class in htsjdk.samtools.fastq: Implementation of a FastqWriter that provides asynchronous output.
AsyncFastqWriter(FastqWriter, int) - Constructor for class htsjdk.samtools.fastq.AsyncFastqWriter
AsyncVariantContextWriter - Class in htsjdk.variant.variantcontext.writer: AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output.
AsyncVariantContextWriter(VariantContextWriter) - Constructor for class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter: Creates a new AsyncVariantContextWriter wrapping the provided VariantContextWriter.
AsyncVariantContextWriter(VariantContextWriter, int) - Constructor for class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter: Creates an AsyncVariantContextWriter wrapping the provided VariantContextWriter and using the specified queue size for buffer VariantContexts.
atEoln() - Method in class htsjdk.samtools.util.FastLineReader
AtomicInt(VCFCompoundHeaderLine, Map<String, Integer>) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.AtomicInt
attribute(String, Object) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder: This genotype has this attribute key / value pair.
attribute(String, Object) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder: Puts the key -> value mapping into this builder's attributes
attributes(Map<String, Object>) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder: This genotype has these attributes.
attributes(Map<String, ?>) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder: Tells this builder to use this map of attributes for the resulting VariantContext.
attributesEqual(AbstractSAMHeaderRecord) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord: For use in the equals() method of the concrete class.
attributesHashCode() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord: For use in the hashCode() method of the concrete class.
available() - Method in class htsjdk.samtools.cram.io.CountingInputStream
available() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
available() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
available() - Method in class htsjdk.samtools.util.CoordSpanInputSteam: Returns how many bytes are left in the current chunk.
available() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream

B

b - Variable in class htsjdk.samtools.util.Tuple
b - Variable in class htsjdk.tribble.util.TabixUtils.TIndex
BAM_FILE_EXTENSION - Static variable in class htsjdk.samtools.BamFileIoUtils
BAM_FLAGS() - Constructor for class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
BAM_LIDX_SHIFT - Static variable in class htsjdk.samtools.LinearIndex
BAM_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
BamFileIoUtils - Class in htsjdk.samtools
BamFileIoUtils() - Constructor for class htsjdk.samtools.BamFileIoUtils
BAMFileSpan - Class in htsjdk.samtools: An ordered list of chunks, capable of representing a set of discontiguous regions in the BAM file.
BAMFileSpan() - Constructor for class htsjdk.samtools.BAMFileSpan: Create a new empty list of chunks.
BAMFileSpan(Chunk) - Constructor for class htsjdk.samtools.BAMFileSpan: Convenience constructor to construct a BAM file span from a single chunk.
BAMFileSpan(List<Chunk>) - Constructor for class htsjdk.samtools.BAMFileSpan: Create a new chunk list from the given list of chunks.
BAMIndex - Interface in htsjdk.samtools: A basic interface for querying BAM indices.
BAMIndexer - Class in htsjdk.samtools: Class for both constructing BAM index content and writing it out.
BAMIndexer(File, SAMFileHeader) - Constructor for class htsjdk.samtools.BAMIndexer
BAMIndexer(OutputStream, SAMFileHeader) - Constructor for class htsjdk.samtools.BAMIndexer: Prepare to index a BAM.
BAMIndexMetaData - Class in htsjdk.samtools: Metadata about the bam index contained within the bam index.
BAMIndexSuffix - Static variable in interface htsjdk.samtools.BAMIndex
BamIndexValidator - Class in htsjdk.samtools: Class to validate (at two different levels of thoroughness) the index for a BAM file.
BamIndexValidator() - Constructor for class htsjdk.samtools.BamIndexValidator
BamIndexValidator.IndexValidationStringency - Enum in htsjdk.samtools
BAMQueryMultipleIntervalsIteratorFilter - Class in htsjdk.samtools: Filters out records that do not match any of the given intervals and query type.
BAMQueryMultipleIntervalsIteratorFilter(QueryInterval[], boolean) - Constructor for class htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter
BAMRecord - Class in htsjdk.samtools: Wrapper class for binary BAM records.
BAMRecord(SAMFileHeader, int, int, short, short, int, int, int, int, int, int, int, byte[]) - Constructor for class htsjdk.samtools.BAMRecord: Create a new BAM Record.
BAMRecordCodec - Class in htsjdk.samtools: Class for translating between in-memory and disk representation of BAMRecord.
BAMRecordCodec(SAMFileHeader) - Constructor for class htsjdk.samtools.BAMRecordCodec
BAMRecordCodec(SAMFileHeader, SAMRecordFactory) - Constructor for class htsjdk.samtools.BAMRecordCodec
base(byte, byte) - Method in class htsjdk.samtools.cram.structure.SubstitutionMatrix
BASE_URL_FOR_HTTP_TESTS - Static variable in class htsjdk.samtools.util.TestUtil: Base url where all test files for http tests are found
baseAndProbDiffToSqValue(SQTagUtil.SQBase, byte) - Static method in class htsjdk.samtools.SQTagUtil: Compress a base and a log probabiliy difference (-10log10(p3/p2)) into a single byte so that it can be output in a SAMRecord's SQ field.
baseAndProbDiffToSqValue(int, byte) - Static method in class htsjdk.samtools.SQTagUtil: Compress a base and a log probabiliy difference (-10log10(p3/p2)) into a single byte so that it can be output in a SAMRecord's SQ field.
baseAt(int) - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
baseCategories - Variable in class htsjdk.samtools.cram.lossy.PreservationPolicy
BaseCategory - Class in htsjdk.samtools.cram.lossy
BaseCategoryType - Enum in htsjdk.samtools.cram.lossy
baseCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
baseCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
basename(File) - Static method in class htsjdk.samtools.util.IOUtil: Returns the name of the file minus the extension (i.e.
BaseQualityScore - Class in htsjdk.samtools.cram.encoding.readfeatures: A read feature representing a single quality score in a read.
BaseQualityScore(int, byte) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
Bases - Class in htsjdk.samtools.cram.encoding.readfeatures
Bases() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Bases
Bases(int, byte[]) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Bases
bases - Variable in class htsjdk.samtools.cram.structure.Container
bases - Variable in class htsjdk.samtools.cram.structure.Slice
BASES - Static variable in class htsjdk.samtools.cram.structure.SubstitutionMatrix
basesCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
basesEqual(byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil: Efficiently compare two IUPAC base codes, simply returning true if they are equal (ignoring case), without considering the set relationships between ambiguous codes.
basesMatch(byte[]) - Method in class htsjdk.variant.variantcontext.Allele
basesMatch(String) - Method in class htsjdk.variant.variantcontext.Allele
basesMatch(Allele) - Method in class htsjdk.variant.variantcontext.Allele
baseSubstitutionCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
baseSubstitutionCodeCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
BasicFastqWriter - Class in htsjdk.samtools.fastq: In general FastqWriterFactory should be used so that AsyncFastqWriter can be enabled, but there are some cases in which that behavior is explicitly not wanted.
BasicFastqWriter(File) - Constructor for class htsjdk.samtools.fastq.BasicFastqWriter
BasicFastqWriter(File, boolean) - Constructor for class htsjdk.samtools.fastq.BasicFastqWriter
BasicFastqWriter(PrintStream) - Constructor for class htsjdk.samtools.fastq.BasicFastqWriter
BCF2Codec - Class in htsjdk.variant.bcf2: Decode BCF2 files
BCF2Codec() - Constructor for class htsjdk.variant.bcf2.BCF2Codec
BCF2Codec.LazyData - Class in htsjdk.variant.bcf2
BCF2Codec.SitesInfoForDecoding - Class in htsjdk.variant.bcf2
BCF2Decoder - Class in htsjdk.variant.bcf2
BCF2Decoder() - Constructor for class htsjdk.variant.bcf2.BCF2Decoder
BCF2Decoder(byte[]) - Constructor for class htsjdk.variant.bcf2.BCF2Decoder: Create a new decoder ready to read BCF2 data from the byte[] recordBytes, for testing purposes
BCF2Encoder - Class in htsjdk.variant.variantcontext.writer: See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2Encoder() - Constructor for class htsjdk.variant.variantcontext.writer.BCF2Encoder
BCF2FieldEncoder - Class in htsjdk.variant.variantcontext.writer: See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldEncoder.AtomicInt - Class in htsjdk.variant.variantcontext.writer: Specialized int encoder for atomic (non-list) integers
BCF2FieldEncoder.Flag - Class in htsjdk.variant.variantcontext.writer
BCF2FieldEncoder.Float - Class in htsjdk.variant.variantcontext.writer
BCF2FieldEncoder.GenericInts - Class in htsjdk.variant.variantcontext.writer
BCF2FieldEncoder.IntArray - Class in htsjdk.variant.variantcontext.writer
BCF2FieldEncoder.StringOrCharacter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter - Class in htsjdk.variant.variantcontext.writer: See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
BCF2FieldWriter.FTGenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.GenericSiteWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.GenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.GTWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.IGFGenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.IntegerTypeGenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.SiteWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.StaticallyTypeGenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriterManager - Class in htsjdk.variant.variantcontext.writer: See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldWriterManager() - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
BCF2GenotypeFieldDecoders - Class in htsjdk.variant.bcf2: An efficient scheme for building and obtaining specialized genotype field decoders.
BCF2GenotypeFieldDecoders(VCFHeader) - Constructor for class htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders
BCF2GenotypeFieldDecoders.Decoder - Interface in htsjdk.variant.bcf2: Decoder a field (implicit from creation) encoded as typeDescriptor in the decoder object in the GenotypeBuilders one for each sample in order.
BCF2LazyGenotypesDecoder - Class in htsjdk.variant.bcf2: Lazy version of genotypes decoder for BCF2 genotypes
BCF2Type - Enum in htsjdk.variant.bcf2: BCF2 types and associated information
BCF2Utils - Class in htsjdk.variant.bcf2: Common utilities for working with BCF2 files Includes convenience methods for encoding, decoding BCF2 type descriptors (size + type)
BCFVersion - Class in htsjdk.variant.bcf2: Simple holder for BCF version information User: depristo Date: 8/2/12 Time: 2:16 PM
BCFVersion(int, int) - Constructor for class htsjdk.variant.bcf2.BCFVersion
BED - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
BED_EXTENSION - Static variable in class htsjdk.tribble.bed.BEDCodec: Default extension for BED files.
BEDCodec - Class in htsjdk.tribble.bed: Codec for parsing BED file, as described by UCSC See https://genome.ucsc.edu/FAQ/FAQformat.html#format1
BEDCodec() - Constructor for class htsjdk.tribble.bed.BEDCodec: Calls BEDCodec.BEDCodec(StartOffset) with an argument of StartOffset.ONE
BEDCodec(BEDCodec.StartOffset) - Constructor for class htsjdk.tribble.bed.BEDCodec: BED format is 0-based, but Tribble is 1-based.
BEDCodec.StartOffset - Enum in htsjdk.tribble.bed: Indicate whether co-ordinates or 0-based or 1-based.
BEDFeature - Interface in htsjdk.tribble.bed
before(Date) - Method in class htsjdk.samtools.util.RelativeIso8601Date
beg - Variable in class htsjdk.tribble.util.TabixUtils.TIntv
BetaIntegerEncoding - Class in htsjdk.samtools.cram.encoding
BetaIntegerEncoding() - Constructor for class htsjdk.samtools.cram.encoding.BetaIntegerEncoding
BetaIntegerEncoding(int, int) - Constructor for class htsjdk.samtools.cram.encoding.BetaIntegerEncoding
BGZF_ID1 - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BGZF_ID2 - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BGZF_LEN - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
Bin - Class in htsjdk.samtools: An individual bin in a BAM file.
Bin(int, int) - Constructor for class htsjdk.samtools.Bin
bin(int) - Static method in class htsjdk.samtools.cram.lossy.QualityScoreTreatment
BIN_GENOMIC_SPAN - Static variable in class htsjdk.samtools.GenomicIndexUtil: Reports the total amount of genomic data that any bin can index.
binary() - Method in class htsjdk.samtools.util.ftp.FTPClient
BinaryCodec - Class in htsjdk.samtools.util: Encapsulates file representation of various primitive data types.
BinaryCodec(File, boolean) - Constructor for class htsjdk.samtools.util.BinaryCodec: Constructs BinaryCodec from a file and set it's mode to writing or not
BinaryCodec(String, boolean) - Constructor for class htsjdk.samtools.util.BinaryCodec: Constructs BinaryCodec from a file name and set it's mode to writing or not
BinaryCodec(OutputStream) - Constructor for class htsjdk.samtools.util.BinaryCodec: Constructs BinaryCodec from an output stream
BinaryCodec(InputStream) - Constructor for class htsjdk.samtools.util.BinaryCodec: Constructs BinaryCodec from an input stream
BinaryCodec() - Constructor for class htsjdk.samtools.util.BinaryCodec: Ambiguous whether reading or writing until set{In,Out}putStream is called
BinaryFeatureCodec<T extends Feature> - Class in htsjdk.tribble: Implements common methods of FeatureCodecs that read from PositionalBufferedStreams.
BinaryFeatureCodec() - Constructor for class htsjdk.tribble.BinaryFeatureCodec
BinaryTagCodec - Class in htsjdk.samtools: Converter between disk and in-memory representation of a SAMRecord tag.
BinaryTagCodec(BinaryCodec) - Constructor for class htsjdk.samtools.BinaryTagCodec: For writing tags.
binaryToEnum(int) - Static method in enum htsjdk.samtools.CigarOperator
bindings - Variable in class htsjdk.samtools.filter.AbstractJavascriptFilter: javascript bindings
BinList - Class in htsjdk.samtools: Provides a list of all bins which could exist in the BAM file.
BinList(int, BitSet) - Constructor for class htsjdk.samtools.BinList: Create a new BinList over sequenceCount sequences, consisting of the given bins.
BinList(Bin[], int) - Constructor for class htsjdk.samtools.BinningIndexContent.BinList
BinningIndexBuilder - Class in htsjdk.samtools: Builder for a BinningIndexContent object.
BinningIndexBuilder(int, int) - Constructor for class htsjdk.samtools.BinningIndexBuilder
BinningIndexBuilder(int) - Constructor for class htsjdk.samtools.BinningIndexBuilder
BinningIndexBuilder.FeatureToBeIndexed - Interface in htsjdk.samtools: coordinates are 1-based, inclusive
BinningIndexContent - Class in htsjdk.samtools: In-memory representation of the binning index for a single reference.
BinningIndexContent(int, BinningIndexContent.BinList, LinearIndex) - Constructor for class htsjdk.samtools.BinningIndexContent
BinningIndexContent.BinList - Class in htsjdk.samtools: This class is used to encapsulate the list of Bins store in the BAMIndexContent While it is currently represented as an array, we may decide to change it to an ArrayList or other structure
bisulfiteBasesEqual(boolean, byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil: Returns true if the bases are equal OR if the mismatch can be accounted for by bisulfite treatment.
bisulfiteBasesEqual(byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil
bisulfiteBasesMatchWithAmbiguity(boolean, byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil: Same as above, but use readBaseMatchesRefBaseWithAmbiguity instead of basesEqual.
BitCodec<T> - Interface in htsjdk.samtools.cram.encoding: An interface that defines requirements for serializing/deserializing objects into and from a bit stream.
bitFlagsC - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
bitFlagsCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
BitInputStream - Interface in htsjdk.samtools.cram.io: An interface to describe the requirements for reading bit data as opposed to bytes.
BitOutputStream - Interface in htsjdk.samtools.cram.io: An interface to describe the requirements for writing out bits as opposed to bytes.
Block - Class in htsjdk.samtools.cram.structure: Class representing CRAM block concept and some methods to operate with block content.
Block() - Constructor for class htsjdk.samtools.cram.structure.Block
Block - Class in htsjdk.tribble.index: Represents a contiguous block of bytes in a file, defined by a start position and size (in bytes)
Block(long, long) - Constructor for class htsjdk.tribble.index.Block
BLOCK_COMPRESSED_EXTENSIONS - Static variable in class htsjdk.tribble.AbstractFeatureReader
BLOCK_FOOTER_LENGTH - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BLOCK_HEADER_LENGTH - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BLOCK_LENGTH_OFFSET - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BlockCompressedFilePointerUtil - Class in htsjdk.samtools.util: Static for manipulating virtual file pointers in BGZF files.
BlockCompressedFilePointerUtil() - Constructor for class htsjdk.samtools.util.BlockCompressedFilePointerUtil
BlockCompressedInputStream - Class in htsjdk.samtools.util
BlockCompressedInputStream(InputStream) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream: Note that seek() is not supported if this ctor is used.
BlockCompressedInputStream(InputStream, boolean) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream: Note that seek() is not supported if this ctor is used.
BlockCompressedInputStream(File) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream: Use this ctor if you wish to call seek()
BlockCompressedInputStream(URL) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
BlockCompressedInputStream(SeekableStream) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream: For providing some arbitrary data source.
BlockCompressedInputStream.FileTermination - Enum in htsjdk.samtools.util
BlockCompressedOutputStream - Class in htsjdk.samtools.util: Writer for a file that is a series of gzip blocks (BGZF format).
BlockCompressedOutputStream(String) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream: Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default DeflaterFactory, see BlockCompressedOutputStream.getDefaultDeflaterFactory().
BlockCompressedOutputStream(File) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream: Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default DeflaterFactory, see BlockCompressedOutputStream.getDefaultDeflaterFactory().
BlockCompressedOutputStream(String, int) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream: Prepare to compress at the given compression level Note: this constructor uses the default DeflaterFactory, see BlockCompressedOutputStream.getDefaultDeflaterFactory().
BlockCompressedOutputStream(File, int) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream: Prepare to compress at the given compression level
BlockCompressedOutputStream(File, int, DeflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream: Prepare to compress at the given compression level
BlockCompressedOutputStream(OutputStream, File) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream: Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default DeflaterFactory, see BlockCompressedOutputStream.getDefaultDeflaterFactory().
BlockCompressedOutputStream(OutputStream, File, int) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream: Note: this constructor uses the default DeflaterFactory, see BlockCompressedOutputStream.getDefaultDeflaterFactory().
BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream: Creates the output stream.
BlockCompressedStreamConstants - Class in htsjdk.samtools.util: Constants shared by BlockCompressed{Input,Output}Stream classes
BlockCompressedStreamConstants() - Constructor for class htsjdk.samtools.util.BlockCompressedStreamConstants
BlockCompressionMethod - Enum in htsjdk.samtools.cram.structure
BlockContentType - Enum in htsjdk.samtools.cram.structure
blockCopyBamFile(File, OutputStream, boolean, boolean) - Static method in class htsjdk.samtools.BamFileIoUtils: Copy data from a BAM file to an OutputStream by directly copying the gzip blocks
blockCount - Variable in class htsjdk.samtools.cram.structure.Container
BlockGunzipper - Class in htsjdk.samtools.util: Alternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[].
BlockGunzipper() - Constructor for class htsjdk.samtools.util.BlockGunzipper
blockIsFullyDecoded() - Method in class htsjdk.variant.bcf2.BCF2Decoder
blocks - Variable in class htsjdk.samtools.cram.structure.Container: Container data
BlockStats() - Constructor for class htsjdk.tribble.index.AbstractIndex.BlockStats
breakIntervalsAtBandMultiples(List<Interval>, int) - Static method in class htsjdk.samtools.util.IntervalList: Given a list of Intervals and a band multiple, this method will return a list of Intervals such that all of the intervals do not straddle integer multiples of that band.
BrowseableBAMIndex - Interface in htsjdk.samtools: An index interface with additional functionality for querying and inspecting the structure of a BAM index.
BUFFER_SIZE - Static variable in class htsjdk.samtools.Defaults: Buffer size, in bytes, used whenever reading/writing files or streams.
BufferedLineReader - Class in htsjdk.samtools.util: Implementation of LineReader that is a thin wrapper around BufferedReader.
BufferedLineReader(InputStream) - Constructor for class htsjdk.samtools.util.BufferedLineReader
BufferedLineReader(InputStream, int) - Constructor for class htsjdk.samtools.util.BufferedLineReader
build(List<CramCompressionRecord>, SubstitutionMatrix, boolean) - Method in class htsjdk.samtools.cram.build.CompressionHeaderFactory: Decides on compression methods to use for the given records.
build() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder: Validate and build the VariantContextWriter.
buildAlleleStrings(VariantContext) - Method in class htsjdk.variant.vcf.VCFEncoder
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.BetaIntegerEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in interface htsjdk.samtools.cram.encoding.Encoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.ExternalByteArrayEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.ExternalByteEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.ExternalIntegerEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.ExternalLongEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.GammaIntegerEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.GolombIntegerEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.GolombLongEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.GolombRiceIntegerEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanByteEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.NullEncoding
buildCodec(Map<Integer, InputStream>, Map<Integer, ExposedByteArrayOutputStream>) - Method in class htsjdk.samtools.cram.encoding.SubexponentialIntegerEncoding
buildContainer(List<CramCompressionRecord>) - Method in class htsjdk.samtools.cram.build.ContainerFactory
buildHeaderTime - Variable in class htsjdk.samtools.cram.structure.Container
buildNewCore(byte[]) - Static method in class htsjdk.samtools.cram.structure.Block: Create a new core block with the given uncompressed content.
buildNewFileHeaderBlock(byte[]) - Static method in class htsjdk.samtools.cram.structure.Block: Create a new core block with the given uncompressed content.
buildNewSliceHeaderBlock(byte[]) - Static method in class htsjdk.samtools.cram.structure.Block: Create a new slice header block with the given uncompressed content.
buildReader(AbstractReader, BitInputStream, Map<Integer, InputStream>, CompressionHeader, int) - Method in class htsjdk.samtools.cram.encoding.reader.DataReaderFactory
buildSlicesTime - Variable in class htsjdk.samtools.cram.structure.Container
buildTree(int[], T[]) - Static method in class htsjdk.samtools.cram.encoding.huffman.HuffmanCode
buildWriter(BitOutputStream, Map<Integer, ExposedByteArrayOutputStream>, CompressionHeader, int) - Method in class htsjdk.samtools.cram.encoding.writer.DataWriterFactory
byEnd - Static variable in class htsjdk.samtools.cram.CRAIEntry
byFirstTwoChars(String) - Static method in enum htsjdk.samtools.cram.structure.EncodingKey
byStart - Static variable in class htsjdk.samtools.cram.CRAIEntry
byStartDesc - Static variable in class htsjdk.samtools.cram.CRAIEntry
BYTE_SPACE_SIZE - Static variable in class htsjdk.samtools.cram.build.CompressionHeaderFactory
ByteArrayLenEncoding - Class in htsjdk.samtools.cram.encoding
ByteArrayLenEncoding() - Constructor for class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
ByteArraySeekableStream - Class in htsjdk.samtools.seekablestream: Created by vadim on 23/03/2015.
ByteArraySeekableStream(byte[]) - Constructor for class htsjdk.samtools.seekablestream.ByteArraySeekableStream
ByteArrayStopCodec(byte, InputStream, OutputStream) - Constructor for class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding.ByteArrayStopCodec
ByteArrayStopEncoding - Class in htsjdk.samtools.cram.encoding
ByteArrayStopEncoding() - Constructor for class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding
ByteArrayStopEncoding.ByteArrayStopCodec - Class in htsjdk.samtools.cram.encoding
bytes - Variable in class htsjdk.variant.bcf2.BCF2Codec.LazyData
bytesToHexString(byte[]) - Static method in class htsjdk.samtools.util.StringUtil: Convert a byte array into a String hex representation.
bytesToString(byte[]) - Static method in class htsjdk.samtools.util.StringUtil
bytesToString(byte[], int, int) - Static method in class htsjdk.samtools.util.StringUtil
byteToChar(byte) - Static method in class htsjdk.samtools.util.StringUtil: Convert ASCII byte to ASCII char.
bzip2(byte[]) - Static method in class htsjdk.samtools.cram.io.ExternalCompression: Compress a byte array into BZIP2 blob.

C

c - Static variable in class htsjdk.samtools.util.SequenceUtil: Byte typed variables for all normal bases.
C - Static variable in class htsjdk.samtools.util.SequenceUtil: Byte typed variables for all normal bases.
calculateAltAlleleFrequency(VariantContext) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils: Computes the alternate allele frequency at the provided VariantContext by dividing its "AN" by its "AC".
calculateAnyploidPLcache(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods: Calculate the cache of allele indices for each PL index for a ploidy.
calculateChromosomeCounts(VariantContext, Map<String, Object>, boolean) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils: Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
calculateChromosomeCounts(VariantContext, Map<String, Object>, boolean, Set<String>) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils: Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
calculateChromosomeCounts(VariantContextBuilder, boolean) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils: Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper chromosome-based VCF tags based on the current VC produced by builder.make()
calculateChromosomeCounts(VariantContextBuilder, boolean, Set<String>) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils: Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper chromosome-based VCF tags based on the current VC produced by builder.make()
calculateGc(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculates the fraction of bases that are G/C in the sequence.
calculateMD5(byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
calculateMD5String(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
calculateMD5String(byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
calculateMdAndNmTags(SAMRecord, byte[], boolean, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculate MD and NM similarly to Samtools, except that N->N is a match.
calculatePLindex(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
calculateReadGroupRecordChecksum(File, File) - Static method in class htsjdk.samtools.SAMUtils: Calculate a hash code from identifying information in the RG (read group) records in a SAM file's header.
calculateSamNmTag(SAMRecord, byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see readBaseMatchesRefBaseWithAmbiguity method).
calculateSamNmTag(SAMRecord, byte[], int) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see readBaseMatchesRefBaseWithAmbiguity method).
calculateSamNmTag(SAMRecord, byte[], int, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see readBaseMatchesRefBaseWithAmbiguity method).
calculateSamNmTagFromCigar(SAMRecord) - Static method in class htsjdk.samtools.util.SequenceUtil: Attempts to calculate the predefined NM tag from the SAM spec using the cigar string alone.
calcVCFGenotypeKeys(VCFHeader) - Method in class htsjdk.variant.variantcontext.VariantContext
canAdd() - Method in class htsjdk.samtools.util.DiskBackedQueue
canCreate() - Method in enum htsjdk.tribble.index.IndexFactory.IndexType
canCreateIndexedFastaReader(File) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
canCreateIndexedFastaReader(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
canDecode(String) - Method in class htsjdk.tribble.bed.BEDCodec
canDecode(String) - Method in class htsjdk.tribble.example.ExampleBinaryCodec
canDecode(String) - Method in interface htsjdk.tribble.FeatureCodec: This function returns true iff the File potentialInput can be parsed by this codec.
canDecode(String) - Method in class htsjdk.tribble.gelitext.GeliTextCodec: Deprecated.
canDecode(String) - Method in class htsjdk.variant.bcf2.BCF2Codec
canDecode(String) - Method in class htsjdk.variant.vcf.VCF3Codec
canDecode(String) - Method in class htsjdk.variant.vcf.VCFCodec
canDecodeFile(String, String) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec
canEmit() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer: Returns true if we can return the next record (it has been examined).
CANNOT_SEEK_STREAM_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
captureAllTags - Variable in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
captureReadNames - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
captureTags - Variable in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
CC - Variable in class htsjdk.samtools.SAMTagUtil
CHAINED_DESCRIPTION - Static variable in class htsjdk.samtools.DownsamplingIteratorFactory
chainSAMProgramRecord(SAMFileHeader, SAMProgramRecord) - Static method in class htsjdk.samtools.SAMUtils: Chains program in front of the first "head" item in the list of SAMProgramRecords in header.
characterToEnum(int) - Static method in enum htsjdk.samtools.CigarOperator
charsToBytes(char[], int, int, byte[], int) - Static method in class htsjdk.samtools.util.StringUtil: Convert chars to bytes merely by casting
charToByte(char) - Static method in class htsjdk.samtools.util.StringUtil: Convert ASCII char to byte.
checkError() - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
checkError() - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
checkError() - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter
checkHeaderAndEOF(File) - Static method in class htsjdk.samtools.cram.build.CramIO: Check if the file: 1) contains proper CRAM header.
checkIfInitialized() - Static method in class htsjdk.samtools.sra.SRAAccession: Tries to initialize SRA.
checkImmutability() - Method in class htsjdk.variant.variantcontext.GenotypesContext
checkMaxEnd() - Method in class htsjdk.samtools.util.IntervalTree.Node
checkMaxEnds() - Method in class htsjdk.samtools.util.IntervalTree: This method is only for debugging.
checksum - Variable in class htsjdk.samtools.cram.structure.Container
checkTermination(File) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
chr - Variable in class htsjdk.tribble.bed.SimpleBEDFeature
chr(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder: Tells us that the resulting VariantContext should have the specified contig chr
chr2tid(String) - Method in class htsjdk.tribble.readers.TabixReader: return chromosome ID or -1 if it is unknown
ChrIndex - Interface in htsjdk.tribble.index: Represents an index on a specific chromosome
ChrIndex() - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex: Default constructor needed for factory methods -- DO NOT REMOVE
ChrIndex(String) - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
ChrIndex() - Constructor for class htsjdk.tribble.index.linear.LinearIndex.ChrIndex: Default constructor needed for factory methods -- DO NOT REMOVE
chrIndices - Variable in class htsjdk.tribble.index.AbstractIndex: the map of our chromosome bins
Chunk - Class in htsjdk.samtools: A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index.
Chunk(long, long) - Constructor for class htsjdk.samtools.Chunk
Cigar - Class in htsjdk.samtools: A list of CigarElements, which describes how a read aligns with the reference.
Cigar() - Constructor for class htsjdk.samtools.Cigar
Cigar(List<CigarElement>) - Constructor for class htsjdk.samtools.Cigar
CIGAR_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
cigarArrayFromElements(List<CigarElement>) - Static method in class htsjdk.samtools.util.CigarUtil
cigarArrayFromString(String) - Static method in class htsjdk.samtools.util.CigarUtil
CigarElement - Class in htsjdk.samtools: One component of a cigar string.
CigarElement(int, CigarOperator) - Constructor for class htsjdk.samtools.CigarElement
cigarMapsNoBasesToRef(Cigar) - Static method in class htsjdk.samtools.SAMUtils: Determines if a cigar has any element that both consumes read bases and consumes reference bases (e.g.
CigarOperator - Enum in htsjdk.samtools: The operators that can appear in a cigar string, and information about their disk representations.
cigarStringFromArray(char[]) - Static method in class htsjdk.samtools.util.CigarUtil
CigarUtil - Class in htsjdk.samtools.util
CigarUtil() - Constructor for class htsjdk.samtools.util.CigarUtil
cleanup() - Method in class htsjdk.samtools.util.SortingCollection: Delete any temporary files.
cleanup() - Method in class htsjdk.samtools.util.SortingLongCollection: Delete any temporary files.
clear() - Method in class htsjdk.samtools.cram.common.IntHashMap: Clears this hashtable so that it contains no keys.
clear() - Method in class htsjdk.samtools.util.DiskBackedQueue
clear() - Method in class htsjdk.samtools.util.IntervalTree: Remove all entries.
clear() - Method in class htsjdk.samtools.util.IntervalTreeMap
clear() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
clear() - Method in class htsjdk.variant.variantcontext.GenotypesContext
clearAttributes() - Method in class htsjdk.samtools.BAMRecord: Removes all attributes.
clearAttributes() - Method in class htsjdk.samtools.SAMRecord: Removes all attributes.
clearAttributes() - Method in class htsjdk.samtools.sra.SRALazyRecord
clearAttributes() - Method in class htsjdk.variant.variantcontext.CommonInfo
clearCache() - Method in class htsjdk.samtools.cram.ref.ReferenceSource
clearIndexCreator() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder: Do not pass an IndexCreator to the next VariantContextWriter created by this builder.
clearOptions() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder: Remove all options from the set of Options for the VariantContextWriterBuilder.
clipOverlappingAlignedBases(SAMRecord, boolean) - Static method in class htsjdk.samtools.SAMUtils: Returns a (possibly new) record that has been clipped if isa mapped paired and has overlapping bases with its mate.
clipOverlappingAlignedBases(SAMRecord, int, boolean) - Static method in class htsjdk.samtools.SAMUtils: Returns a (possibly new) SAMRecord with the given number of bases soft-clipped at the end of the read if is a mapped paired and has overlapping bases with its mate.
clone() - Method in class htsjdk.samtools.BAMFileSpan: Deep clone the given chunk list.
clone() - Method in class htsjdk.samtools.BAMRecordCodec
clone() - Method in class htsjdk.samtools.Chunk
clone() - Method in class htsjdk.samtools.cram.CRAIEntry
clone() - Method in class htsjdk.samtools.cram.structure.CramHeader: Copy the CRAM header into a new CramHeader object.
clone() - Method in class htsjdk.samtools.SAMFileHeader
clone() - Method in class htsjdk.samtools.SAMFileWriterFactory
clone() - Method in class htsjdk.samtools.SAMRecord: Note that this does a shallow copy of everything, except for the attribute list, for which a copy of the list is made, but the attributes themselves are copied by reference.
clone() - Method in class htsjdk.samtools.SAMSequenceRecord
clone() - Method in class htsjdk.samtools.sra.SRALazyRecord: Performs a deep copy of the SAMRecord and detaches a copy from NGS iterator
clone() - Method in class htsjdk.samtools.util.Interval
clone() - Method in class htsjdk.samtools.util.RelativeIso8601Date
clone() - Method in interface htsjdk.samtools.util.SortingCollection.Codec: Must return a cloned copy of the codec that can be used independently of the original instance.
clone() - Method in class htsjdk.tribble.index.tabix.TabixFormat
clone() - Method in class htsjdk.variant.vcf.VCFRecordCodec
cloneValue() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
close() - Method in class htsjdk.samtools.AbstractBAMFileIndex: Close this index and release any associated resources.
close() - Method in interface htsjdk.samtools.BAMIndex: Close the index and release any associated resources.
close() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
close() - Method in class htsjdk.samtools.cram.io.CountingInputStream
close() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
close() - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
close() - Method in class htsjdk.samtools.CRAMFileReader
close() - Method in class htsjdk.samtools.CRAMIterator
close() - Method in class htsjdk.samtools.DownsamplingIterator: Does nothing.
close() - Method in class htsjdk.samtools.DuplicateSetIterator
close() - Method in class htsjdk.samtools.fastq.BasicFastqWriter
close() - Method in class htsjdk.samtools.fastq.FastqReader
close() - Method in interface htsjdk.samtools.fastq.FastqWriter
close() - Method in class htsjdk.samtools.filter.FilteringSamIterator
close() - Method in class htsjdk.samtools.MergingSamRecordIterator: Close down all open iterators.
close() - Method in class htsjdk.samtools.reference.FastaSequenceFile: It's good to call this to free up memory.
close() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
close() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
close() - Method in class htsjdk.samtools.reference.ReferenceSequenceFileWalker
close() - Method in interface htsjdk.samtools.SAMFileWriter: Must be called to flush or file will likely be defective.
close() - Method in class htsjdk.samtools.SAMFileWriterImpl: Must be called or else file will likely be defective.
close() - Method in class htsjdk.samtools.SamReader.AssertingIterator
close() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
close() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
close() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
close() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
close() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableStream
close() - Method in class htsjdk.samtools.sra.SRAAlignmentIterator
close() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
close() - Method in class htsjdk.samtools.SRAFileReader
close() - Method in class htsjdk.samtools.SRAIndex
close() - Method in class htsjdk.samtools.SRAIterator
close() - Method in class htsjdk.samtools.util.AbstractAsyncWriter: Attempts to finish draining the queue and then calls synchronouslyClose() to allow implementation to do any one time clean up.
close() - Method in class htsjdk.samtools.util.AbstractLocusIterator: Closes inner SamIterator.
close() - Method in class htsjdk.samtools.util.AsciiWriter: flushes and closes underlying OutputStream.
close() - Method in class htsjdk.samtools.util.AsyncBufferedIterator
close() - Method in class htsjdk.samtools.util.BinaryCodec: Close the appropriate stream
close() - Method in class htsjdk.samtools.util.BlockCompressedInputStream: Closes the underlying InputStream or RandomAccessFile
close() - Method in class htsjdk.samtools.util.BlockCompressedOutputStream: close() must be called in order to flush any remaining buffered bytes.
close() - Method in class htsjdk.samtools.util.BufferedLineReader
close() - Method in interface htsjdk.samtools.util.CloseableIterator: Should be implemented to close/release any underlying resources.
close(Object) - Static method in class htsjdk.samtools.util.CloserUtil: Calls close() on obj if it implements Closeable
close(List<? extends Object>) - Static method in class htsjdk.samtools.util.CloserUtil: Calls close() on all elements of objs that implement Closeable
close() - Method in class htsjdk.samtools.util.CoordSpanInputSteam
close() - Method in class htsjdk.samtools.util.DelegatingIterator
close() - Method in class htsjdk.samtools.util.FastLineReader
close() - Method in class htsjdk.samtools.util.ftp.FTPStream
close() - Method in class htsjdk.samtools.util.IterableOnceIterator: Does nothing, intended to be overridden when needed.
close() - Method in interface htsjdk.samtools.util.LineReader
close() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
close() - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
close() - Method in class htsjdk.samtools.util.MergingIterator: Closes every CloseableIterator in this MergingIterator.
close() - Method in class htsjdk.samtools.util.PeekableIterator: Closes the underlying iterator.
close() - Method in class htsjdk.samtools.util.PositionalOutputStream
close() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer: Close IO resources associated with each underlying BufferBlock
close() - Method in class htsjdk.samtools.util.StringLineReader
close(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec
close(PositionalBufferedStream) - Method in class htsjdk.tribble.BinaryFeatureCodec
close(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec: Adapter method that closes the provided SOURCE.
close() - Method in interface htsjdk.tribble.FeatureReader
close() - Method in class htsjdk.tribble.readers.AsciiLineReader
close() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
close() - Method in class htsjdk.tribble.readers.LineIteratorImpl
close() - Method in interface htsjdk.tribble.readers.LineReader
close() - Method in class htsjdk.tribble.readers.LongLineBufferedReader
close() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
close() - Method in class htsjdk.tribble.readers.SynchronousLineReader
close() - Method in class htsjdk.tribble.readers.TabixIteratorLineReader
close() - Method in class htsjdk.tribble.readers.TabixReader
close() - Method in class htsjdk.tribble.TabixFeatureReader
close() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
close() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator
close() - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter: attempt to close the VCF file
close() - Method in class htsjdk.variant.vcf.VCFFileReader
CloseableIterator<T> - Interface in htsjdk.samtools.util: This interface is used by iterators that use releasable resources during iteration.
CloseableTribbleIterator<T extends Feature> - Interface in htsjdk.tribble: The basic iterator we use in Tribble, which allows closing and basic iteration.
closeAllInstances() - Static method in class htsjdk.samtools.seekablestream.SeekableFileStream
closeAllInstances() - Static method in class htsjdk.samtools.seekablestream.SeekablePathStream
closeDataStream() - Method in class htsjdk.samtools.util.ftp.FTPClient
CloserUtil - Class in htsjdk.samtools.util: Utility to close things that implement Closeable WARNING: This should only be used for Closeable things open for read, because it ignores exceptions, and the caller will probably want to know about exceptions when closing a file being written to, because this may indicate a failure to flush.
CloserUtil() - Constructor for class htsjdk.samtools.util.CloserUtil
CM - Variable in class htsjdk.samtools.SAMTagUtil
code(byte, byte) - Method in class htsjdk.samtools.cram.structure.SubstitutionMatrix
codec - Variable in class htsjdk.tribble.AbstractFeatureReader
CodecLineParsingException - Exception in htsjdk.tribble.exception: Class CodecLineParsingException a generic exception we use if the codec has trouble parsing the line its given
CodecLineParsingException(Throwable) - Constructor for exception htsjdk.tribble.exception.CodecLineParsingException
CodecLineParsingException(String, Throwable) - Constructor for exception htsjdk.tribble.exception.CodecLineParsingException
CodecLineParsingException(String) - Constructor for exception htsjdk.tribble.exception.CodecLineParsingException
CodecLineParsingException() - Constructor for exception htsjdk.tribble.exception.CodecLineParsingException
CodeUtil - Class in htsjdk.samtools.util: Miscellaneous util methods that don't fit anywhere else.
CodeUtil() - Constructor for class htsjdk.samtools.util.CodeUtil
collapseStringList(List<String>) - Static method in class htsjdk.variant.bcf2.BCF2Utils: Collapse multiple strings into a comma separated list ["s1", "s2", "s3"] => ",s1,s2,s3"
CollectionUtil - Class in htsjdk.samtools.util: Small utility methods for dealing with collection classes.
CollectionUtil() - Constructor for class htsjdk.samtools.util.CollectionUtil
CollectionUtil.DefaultingMap<K,V> - Class in htsjdk.samtools.util: A defaulting map, which returns a default value when a value that does not exist in the map is looked up.
CollectionUtil.DefaultingMap.Factory<V,K> - Interface in htsjdk.samtools.util
CollectionUtil.MultiMap<K,V> - Class in htsjdk.samtools.util: Simple multi-map for convenience of storing collections in map values.
CollectionUtil.Partitioner<V,K> - Class in htsjdk.samtools.util: Deprecated.
use Collectors.groupingBy instead
colorCache - Static variable in class htsjdk.tribble.util.ParsingUtils
combineMapqs(int, int) - Static method in class htsjdk.samtools.SAMUtils: Hokey algorithm for combining two MAPQs into values that are comparable, being cognizant of the fact that in MAPQ world, 1 > 255 > 0.
COMMAND_LINE_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
COMMENT_PREFIX - Static variable in class htsjdk.samtools.SAMTextHeaderCodec
CommonInfo - Class in htsjdk.variant.variantcontext: Common utility routines for VariantContext and Genotype
CommonInfo(String, double, Set<String>, Map<String, Object>) - Constructor for class htsjdk.variant.variantcontext.CommonInfo
commonInfo - Variable in class htsjdk.variant.variantcontext.VariantContext
ComparableTuple<A extends java.lang.Comparable<A>,B extends java.lang.Comparable<B>> - Class in htsjdk.samtools.util: A simple extension of the Tuple class that, for comparable Types, allows comparing Tuples of non-null elements.
ComparableTuple(A, B) - Constructor for class htsjdk.samtools.util.ComparableTuple
comparator() - Method in class htsjdk.samtools.util.Histogram: Returns the comparator used to order the keys in this histogram, or null if this histogram uses the natural ordering of its keys.
compare(SAMRecord, SAMRecord, DuplicateScoringStrategy.ScoringStrategy, boolean) - Static method in class htsjdk.samtools.DuplicateScoringStrategy: Compare two records based on their duplicate scores.
compare(SAMRecord, SAMRecord, DuplicateScoringStrategy.ScoringStrategy) - Static method in class htsjdk.samtools.DuplicateScoringStrategy: Compare two records based on their duplicate scores.
compare(T, T) - Method in class htsjdk.samtools.SAMHeaderRecordComparator
compare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordCoordinateComparator
compare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordDuplicateComparator: Most stringent comparison.
compare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordQueryHashComparator: Compares two records based on an integer hash of their read name's.
compare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordQueryNameComparator
compare(long, long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
compare(T, T) - Method in class htsjdk.samtools.util.LocusComparator
compare(VariantContext, VariantContext) - Method in class htsjdk.variant.variantcontext.VariantContextComparator
compareDoubles(double, double) - Static method in class htsjdk.variant.utils.GeneralUtils: Compares double values for equality (within 1e-6), or inequality.
compareDoubles(double, double, double) - Static method in class htsjdk.variant.utils.GeneralUtils: Compares double values for equality (within epsilon), or inequality.
compareIntervalToRecord(QueryInterval, SAMRecord) - Static method in class htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter
compareMapqs(int, int) - Static method in class htsjdk.samtools.SAMUtils
compareReadNames(String, String) - Static method in class htsjdk.samtools.SAMRecordQueryNameComparator: Encapsulate algorithm for comparing read names in queryname-sorted file, since there have been conversations about changing the behavior.
compareTo(Bin) - Method in class htsjdk.samtools.Bin: Compare two bins to see what ordering they should appear in.
compareTo(Chunk) - Method in class htsjdk.samtools.Chunk
compareTo(Version) - Method in class htsjdk.samtools.cram.common.Version: Compare with another version.
compareTo(CRAIEntry) - Method in class htsjdk.samtools.cram.CRAIEntry
compareTo(HuffmanTree<T>) - Method in class htsjdk.samtools.cram.encoding.huffman.HuffmanTree
compareTo(ReadTag) - Method in class htsjdk.samtools.cram.structure.ReadTag
compareTo(QueryInterval) - Method in class htsjdk.samtools.QueryInterval
compareTo(ComparableTuple<A, B>) - Method in class htsjdk.samtools.util.ComparableTuple
compareTo(Interval) - Method in class htsjdk.samtools.util.Interval: Sort based on sequence.compareTo, then start pos, then end pos with null objects coming lexically last
compareTo(Date) - Method in class htsjdk.samtools.util.RelativeIso8601Date
compareTo(Object) - Method in class htsjdk.tribble.index.interval.Interval
compareTo(TabixReader.TPair64) - Method in class htsjdk.tribble.readers.TabixReader.TPair64
compareTo(TabixUtils.TPair64) - Method in class htsjdk.tribble.util.TabixUtils.TPair64
compareTo(Allele) - Method in class htsjdk.variant.variantcontext.Allele
compareTo(Genotype) - Method in class htsjdk.variant.variantcontext.Genotype: comparable genotypes -> compareTo on the sample names
compareTo(Object) - Method in class htsjdk.variant.vcf.VCFContigHeaderLine: IT IS CRITICAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER
compareTo(Object) - Method in class htsjdk.variant.vcf.VCFHeaderLine
compareToFilter(SAMRecord) - Method in class htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter
compatibleWith(Version) - Method in class htsjdk.samtools.cram.common.Version
compBitFlagsC - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
complement(byte) - Static method in class htsjdk.samtools.util.SequenceUtil: Returns the complement of a single byte.
ComponentMethods() - Constructor for class htsjdk.tribble.AbstractFeatureReader.ComponentMethods
CompoundFilter - Class in htsjdk.variant.variantcontext.filter: A Predicate on VariantContexts that returns true when either all its sub-predicates are true, or none are false.
CompoundFilter(boolean) - Constructor for class htsjdk.variant.variantcontext.filter.CompoundFilter: A constructor that will determine if this compound filter will require that *all* the included filters pass or *some* of them pass (depending on the requireAll parameter in the constructor).
compress(byte[]) - Method in class htsjdk.samtools.cram.encoding.ExternalCompressor
compress(ByteBuffer, RANS.ORDER, ByteBuffer) - Static method in class htsjdk.samtools.cram.encoding.rans.RANS
compressedBasesToBytes(int, byte[], int) - Static method in class htsjdk.samtools.SAMUtils: Convert from a byte array with basese stored in nybbles, with =, A, C, G, T represented as 0, 1, 2, 4, 8, 15, to a a byte array containing =AaCcGgTtNn represented as ASCII.
COMPRESSION_LEVEL - Static variable in class htsjdk.samtools.Defaults: Compresion level to be used for writing BAM and other block-compressed outputs.
compressionBitFlagsCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
compressionFlags - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
CompressionHeader - Class in htsjdk.samtools.cram.structure
CompressionHeader() - Constructor for class htsjdk.samtools.cram.structure.CompressionHeader
CompressionHeaderFactory - Class in htsjdk.samtools.cram.build: A class responsible for decisions about which encodings to use for a given set of records.
CompressionHeaderFactory() - Constructor for class htsjdk.samtools.cram.build.CompressionHeaderFactory
computeDuplicateScore(SAMRecord, DuplicateScoringStrategy.ScoringStrategy) - Static method in class htsjdk.samtools.DuplicateScoringStrategy: Returns the duplicate score computed from the given fragment.
computeDuplicateScore(SAMRecord, DuplicateScoringStrategy.ScoringStrategy, boolean) - Static method in class htsjdk.samtools.DuplicateScoringStrategy: Returns the duplicate score computed from the given fragment.
computeEndFromAlleles(List<Allele>, int) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
computeEndFromAlleles(List<Allele>, int, int) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder: Compute the end position for this VariantContext from the alleles themselves assigns this builder the stop position computed.
computeEndFromAlleles(List<Allele>, int, int) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils: Compute the end position for this VariantContext from the alleles themselves In the trivial case this is a single BP event and end = start (open intervals) In general the end is start + ref length - 1, handling the case where ref length == 0 However, if alleles contains a symbolic allele then we use endForSymbolicAllele in all cases
computeInsertSize(CramCompressionRecord, CramCompressionRecord) - Static method in class htsjdk.samtools.cram.build.CramNormalizer: The method is similar in semantics to computeInsertSize but operates on CRAM native records instead of SAMRecord objects.
computeInsertSize(SAMRecord, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil: Compute SAMRecord insert size
concatenate(Collection<IntervalList>) - Static method in class htsjdk.samtools.util.IntervalList: A utility function for merging a list of IntervalLists, checks for equal dictionaries.
connect(String) - Method in class htsjdk.samtools.util.ftp.FTPClient: Connects to the given FTP host on the default port.
connect(String, String, UserPasswordInput) - Static method in class htsjdk.samtools.util.ftp.FTPUtils: Connect to an FTP server
cons(T, List<T>) - Static method in class htsjdk.variant.utils.GeneralUtils
CONSTANT_MEMORY_DESCRPTION - Static variable in class htsjdk.samtools.DownsamplingIteratorFactory
consumesReadBases() - Method in enum htsjdk.samtools.CigarOperator: If true, represents that this cigar operator "consumes" bases from the read bases.
consumesReferenceBases() - Method in enum htsjdk.samtools.CigarOperator: If true, represents that this cigar operator "consumes" bases from the reference sequence.
Container - Class in htsjdk.samtools.cram.structure
Container() - Constructor for class htsjdk.samtools.cram.structure.Container
container - Variable in class htsjdk.samtools.CRAMIterator
containerByteSize - Variable in class htsjdk.samtools.cram.structure.Container: Byte size of the content excluding header.
ContainerFactory - Class in htsjdk.samtools.cram.build
ContainerFactory(SAMFileHeader, int) - Constructor for class htsjdk.samtools.cram.build.ContainerFactory
ContainerIO - Class in htsjdk.samtools.cram.structure: Methods to read and write CRAM containers.
ContainerIO() - Constructor for class htsjdk.samtools.cram.structure.ContainerIO
containerOffset - Variable in class htsjdk.samtools.cram.structure.Slice
ContainerParser - Class in htsjdk.samtools.cram.build
ContainerParser(SAMFileHeader) - Constructor for class htsjdk.samtools.cram.build.ContainerParser
containerSize - Variable in class htsjdk.samtools.CRAMContainerStreamWriter
containerStartOffset - Variable in class htsjdk.samtools.cram.CRAIEntry
contains(Object) - Method in class htsjdk.samtools.cram.common.IntHashMap: Tests if some key maps into the specified value in this hashtable.
contains(Object) - Method in class htsjdk.samtools.util.DiskBackedQueue: Not supported.
contains(Interval, String, long) - Static method in class htsjdk.samtools.util.IntervalUtil: Return true if the sequence/position lie in the provided interval.
contains(IntervalList, String, long) - Static method in class htsjdk.samtools.util.IntervalUtil: Return true if the sequence/position lie in the provided interval list.
contains(SamRecordWithOrdinal) - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer: Returns true if this buffer contains the record at the given index, false otherwise
contains(Object) - Method in class htsjdk.variant.variantcontext.GenotypesContext
containsAll(Collection<?>) - Method in class htsjdk.samtools.util.DiskBackedQueue: Not supported.
containsAll(Collection<?>) - Method in class htsjdk.variant.variantcontext.GenotypesContext
containsBase(char) - Method in enum htsjdk.tribble.gelitext.DiploidGenotype: Deprecated.
containsBin(Bin) - Method in class htsjdk.samtools.BinningIndexContent: Does this content have anything in this bin?
containsChromosome(String) - Method in class htsjdk.tribble.index.AbstractIndex
containsChromosome(String) - Method in interface htsjdk.tribble.index.Index
containsChromosome(String) - Method in class htsjdk.tribble.index.tabix.TabixIndex
containsChunks() - Method in class htsjdk.samtools.Bin: Returns whether the bin currently contains chunks.
containsContained(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap: Test if this contains an object that is contained by 'key'
containsKey(int) - Method in class htsjdk.samtools.cram.common.IntHashMap: Tests if the specified object is a key in this hashtable.
containsKey(K) - Method in class htsjdk.samtools.util.Histogram: Return whether this histogram contains the given key.
containsKey(Object) - Method in class htsjdk.samtools.util.IntervalTreeMap
containsKey(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap
containsKey(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap: Determine if the map contains the given key.
containsOperator(CigarOperator) - Method in class htsjdk.samtools.Cigar: returns true if the cigar string contains the given operator
containsOverlapping(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap: Test overlapping interval
containsSample(String) - Method in class htsjdk.variant.variantcontext.GenotypesContext
containsSamples(Collection<String>) - Method in class htsjdk.variant.variantcontext.GenotypesContext
containsValue(Object) - Method in class htsjdk.samtools.cram.common.IntHashMap: Returns true if this HashMap maps one or more keys to this value.
ContentDigests - Class in htsjdk.samtools.cram.digest
ContentDigests.KNOWN_DIGESTS - Enum in htsjdk.samtools.cram.digest
contentIDs - Variable in class htsjdk.samtools.cram.structure.Slice
contig - Variable in class htsjdk.variant.variantcontext.VariantContext: The location of this VariantContext
CONTIG_HEADER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
CONTIG_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
CONTIG_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
convertReadNamesToUpperCase(File, File) - Method in class htsjdk.samtools.example.ExampleSamUsage: Read a SAM or BAM file, convert each read name to upper case, and write a new SAM or BAM file.
convertSolexa_1_3_QualityCharsToPhredBinary(byte[]) - Method in class htsjdk.samtools.util.SolexaQualityConverter: Casava 1.3 stores phred-scaled qualities, but non-standard because they have 64 added to them rather than the standard 33.
convertSolexa_1_3_QualityCharsToPhredBinary(int, int, byte[]) - Method in class htsjdk.samtools.util.SolexaQualityConverter
convertSolexaQualityCharsToPhredBinary(byte[]) - Method in class htsjdk.samtools.util.SolexaQualityConverter: Decodes an array of solexa quality ASCII chars into Phred numeric space.
convertSolexaQualityCharsToPhredChars(byte[]) - Method in class htsjdk.samtools.util.SolexaQualityConverter: Decodes an array of solexa quality ASCII chars into Phred ASCII space.
convertToBinaryTest(File, File, FeatureCodec<FEATURE_TYPE, LineIterator>) - Static method in class htsjdk.tribble.example.ExampleBinaryCodec: Convenience method that creates an ExampleBinaryCodec file from another feature file.
convertToBinaryTest(FeatureReader<FEATURE_TYPE>, OutputStream) - Static method in class htsjdk.tribble.example.ExampleBinaryCodec: Convenience method that creates an ExampleBinaryCodec file from another feature file.
convertToLinearIndexOffset(int) - Static method in class htsjdk.samtools.LinearIndex
CoordinateSortedPairInfoMap<KEY,REC> - Class in htsjdk.samtools: Holds info about a mate pair for use when processing a coordinate sorted file.
CoordinateSortedPairInfoMap(int, CoordinateSortedPairInfoMap.Codec<KEY, REC>) - Constructor for class htsjdk.samtools.CoordinateSortedPairInfoMap
CoordinateSortedPairInfoMap.Codec<KEY,REC> - Interface in htsjdk.samtools: Client must implement this class, which defines the way in which records are written to and read from file.
CoordMath - Class in htsjdk.samtools.util: Static methods that encapsulate the standard SAM way of storing ranges: one-based, with both ends inclusive.
CoordMath() - Constructor for class htsjdk.samtools.util.CoordMath
CoordSpanInputSteam - Class in htsjdk.samtools.util: An input stream that wraps a SeekableStream to produce only bytes specified within coordinates.
CoordSpanInputSteam(SeekableStream, long[]) - Constructor for class htsjdk.samtools.util.CoordSpanInputSteam: Wrap SeekableStream to read only bytes within boundaries specified in the coords array.
copy() - Method in class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue: Creates and returns a shallow copy of the list of tag/values.
copy() - Method in class htsjdk.samtools.SAMBinaryTagAndValue: Creates and returns a shallow copy of the list of tag/values.
copy(Genotype) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder: Copy all of the values for this builder from Genotype g
copy(GenotypesContext) - Static method in class htsjdk.variant.variantcontext.GenotypesContext: Create a freshly allocated GenotypeContext containing the genotypes in toCopy
copy(Collection<Genotype>) - Static method in class htsjdk.variant.variantcontext.GenotypesContext: Create a GenotypesContext containing the genotypes in iteration order contained in toCopy
copy() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
copyDirectoryTree(File, File) - Static method in class htsjdk.samtools.util.IOUtil: Copies a directory tree (all subdirectories and files) recursively to a destination
copyFile(File, File) - Static method in class htsjdk.samtools.util.IOUtil: Copy input to output, overwriting output if it already exists.
copyOf(IntervalList) - Static method in class htsjdk.samtools.util.IntervalList: creates a independent copy of the given IntervalList
copyStream(InputStream, OutputStream) - Static method in class htsjdk.samtools.util.IOUtil: Utility method to copy the contents of input to output.
coreBlock - Variable in class htsjdk.samtools.cram.structure.Slice
countAllele(Allele) - Method in class htsjdk.variant.variantcontext.Genotype: Returns how many times allele appears in this genotype object?
countBases(Collection<Interval>) - Static method in class htsjdk.samtools.util.Interval: Counts the total number of bases a collection of intervals.
countDeletedBases(Cigar) - Static method in class htsjdk.samtools.util.SequenceUtil
countDeletedBases(SAMRecord) - Static method in class htsjdk.samtools.util.SequenceUtil
CountingInputStream - Class in htsjdk.samtools.cram.io: An input stream that counts the bytes read from it.
CountingInputStream(InputStream) - Constructor for class htsjdk.samtools.cram.io.CountingInputStream
countInsertedBases(Cigar) - Static method in class htsjdk.samtools.util.SequenceUtil
countInsertedBases(SAMRecord) - Static method in class htsjdk.samtools.util.SequenceUtil
countMismatches(SAMRecord, byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculates the number of mismatches between the read and the reference sequence provided.
countMismatches(SAMRecord, byte[], int) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculates the number of mismatches between the read and the reference sequence provided.
countMismatches(SAMRecord, byte[], int, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculates the number of mismatches between the read and the reference sequence provided.
countMismatches(SAMRecord, byte[], int, boolean, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
countMismatches(SAMRecord, byte[], boolean) - Static method in class htsjdk.samtools.util.SequenceUtil: Calculates the number of mismatches between the read and the reference sequence provided.
CountRecords - Class in htsjdk.tribble.example: An example of how to index a feature file, and then count all the records in the file.
CountRecords() - Constructor for class htsjdk.tribble.example.CountRecords
coverageAt(int) - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
CP - Variable in class htsjdk.samtools.SAMTagUtil
CQ - Variable in class htsjdk.samtools.SAMTagUtil
CRAI_INDEX_SUFFIX - Static variable in class htsjdk.samtools.cram.CRAIIndex
CRAIEntry - Class in htsjdk.samtools.cram: A class representing CRAI index entry: file and alignment offsets for each slice.
CRAIEntry() - Constructor for class htsjdk.samtools.cram.CRAIEntry
CRAIEntry(String) - Constructor for class htsjdk.samtools.cram.CRAIEntry: Create a CRAI Entry from a serialized CRAI index line.
CRAIIndex - Class in htsjdk.samtools.cram: CRAI index used for CRAM files.
CRAIIndex() - Constructor for class htsjdk.samtools.cram.CRAIIndex
CRAIIndex.CRAIIndexException - Exception in htsjdk.samtools.cram
CRAIIndexException(String) - Constructor for exception htsjdk.samtools.cram.CRAIIndex.CRAIIndexException
CRAIIndexException(NumberFormatException) - Constructor for exception htsjdk.samtools.cram.CRAIIndex.CRAIIndexException
Cram2SamRecordFactory - Class in htsjdk.samtools.cram.build
Cram2SamRecordFactory(SAMFileHeader) - Constructor for class htsjdk.samtools.cram.build.Cram2SamRecordFactory
CRAM_FILE_EXTENSION - Static variable in class htsjdk.samtools.cram.build.CramIO
CRAM_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
CRAM_v2_1 - Static variable in class htsjdk.samtools.cram.common.CramVersions
CRAM_v3 - Static variable in class htsjdk.samtools.cram.common.CramVersions
CramArray - Class in htsjdk.samtools.cram.io: Methods to read and write CRAM array of integers data type.
CramArray() - Constructor for class htsjdk.samtools.cram.io.CramArray
CRAMBAIIndexer - Class in htsjdk.samtools: Class for both constructing BAM index content and writing it out.
CRAMBAIIndexer(File, SAMFileHeader) - Constructor for class htsjdk.samtools.CRAMBAIIndexer: Create a CRAM indexer that writes BAI to a file.
CRAMBAIIndexer(OutputStream, SAMFileHeader) - Constructor for class htsjdk.samtools.CRAMBAIIndexer: Create a CRAM indexer that writes BAI to a stream.
CramCompressionRecord - Class in htsjdk.samtools.cram.structure
CramCompressionRecord() - Constructor for class htsjdk.samtools.cram.structure.CramCompressionRecord
CramCompressionRecord.BAM_FLAGS - Class in htsjdk.samtools.cram.structure
CramContainerIterator - Class in htsjdk.samtools.cram.build: An iterator of CRAM containers read from an InputStream.
CramContainerIterator(InputStream) - Constructor for class htsjdk.samtools.cram.build.CramContainerIterator
CRAMContainerStreamWriter - Class in htsjdk.samtools: Class for writing SAMRecords into a series of CRAM containers on an output stream.
CRAMContainerStreamWriter(OutputStream, OutputStream, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMContainerStreamWriter: Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
CRAMCRAIIndexer - Class in htsjdk.samtools: Indexer for creating/reading/writing a CRAIIndex for a CRAM file/stream.
CRAMCRAIIndexer(OutputStream, SAMFileHeader) - Constructor for class htsjdk.samtools.CRAMCRAIIndexer: Create a CRAMCRAIIndexer that writes to the given output stream.
CRAMException - Exception in htsjdk.samtools.cram: Created by edwardk on 8/13/15.
CRAMException() - Constructor for exception htsjdk.samtools.cram.CRAMException
CRAMException(String) - Constructor for exception htsjdk.samtools.cram.CRAMException
CRAMException(String, Throwable) - Constructor for exception htsjdk.samtools.cram.CRAMException
CRAMException(Throwable) - Constructor for exception htsjdk.samtools.cram.CRAMException
CRAMFileReader - Class in htsjdk.samtools: BAMFileReader analogue for CRAM files.
CRAMFileReader(File, InputStream) - Constructor for class htsjdk.samtools.CRAMFileReader: Create a CRAMFileReader from either a file or input stream using the reference source returned by getDefaultCRAMReferenceSource.
CRAMFileReader(File, InputStream, CRAMReferenceSource) - Constructor for class htsjdk.samtools.CRAMFileReader: Create a CRAMFileReader from either a file or input stream using the supplied reference source.
CRAMFileReader(File, File, CRAMReferenceSource) - Constructor for class htsjdk.samtools.CRAMFileReader: Create a CRAMFileReader from a file and optional index file using the supplied reference source.
CRAMFileReader(File, CRAMReferenceSource) - Constructor for class htsjdk.samtools.CRAMFileReader: Create a CRAMFileReader from a file using the supplied reference source.
CRAMFileReader(InputStream, SeekableStream, CRAMReferenceSource, ValidationStringency) - Constructor for class htsjdk.samtools.CRAMFileReader: Create a CRAMFileReader from an input stream and optional index stream using the supplied reference source and validation stringency.
CRAMFileReader(InputStream, File, CRAMReferenceSource, ValidationStringency) - Constructor for class htsjdk.samtools.CRAMFileReader: Create a CRAMFileReader from an input stream and optional index file using the supplied reference source and validation stringency.
CRAMFileReader(File, File, CRAMReferenceSource, ValidationStringency) - Constructor for class htsjdk.samtools.CRAMFileReader: Create a CRAMFileReader from a CRAM file and optional index file using the supplied reference source and validation stringency.
CRAMFileWriter - Class in htsjdk.samtools
CRAMFileWriter(OutputStream, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMFileWriter: Create a CRAMFileWriter on an output stream.
CRAMFileWriter(OutputStream, OutputStream, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMFileWriter: Create a CRAMFileWriter and optional index on output streams.
CRAMFileWriter(OutputStream, OutputStream, boolean, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMFileWriter: Create a CRAMFileWriter and optional index on output streams.
CramHeader - Class in htsjdk.samtools.cram.structure: A starting object when dealing with CRAM files.
CramHeader(Version, String, SAMFileHeader) - Constructor for class htsjdk.samtools.cram.structure.CramHeader: Create a new CramHeader object with the specified version, id and SAM file header.
CramInt - Class in htsjdk.samtools.cram.io: Methods to read and write CRAM int values as given in the file format specification.
CramInt() - Constructor for class htsjdk.samtools.cram.io.CramInt
CramIO - Class in htsjdk.samtools.cram.build: A collection of methods to open and close CRAM files.
CramIO() - Constructor for class htsjdk.samtools.cram.build.CramIO
CRAMIterator - Class in htsjdk.samtools
CRAMIterator(InputStream, CRAMReferenceSource, ValidationStringency) - Constructor for class htsjdk.samtools.CRAMIterator
CRAMIterator(SeekableStream, CRAMReferenceSource, long[], ValidationStringency) - Constructor for class htsjdk.samtools.CRAMIterator
CRAMIterator(SeekableStream, CRAMReferenceSource, long[]) - Constructor for class htsjdk.samtools.CRAMIterator: Deprecated.
CramNormalizer - Class in htsjdk.samtools.cram.build
CramNormalizer(SAMFileHeader, CRAMReferenceSource) - Constructor for class htsjdk.samtools.cram.build.CramNormalizer
CramRecordReader - Class in htsjdk.samtools.cram.encoding.reader
CramRecordReader(ValidationStringency) - Constructor for class htsjdk.samtools.cram.encoding.reader.CramRecordReader
CRAMReferenceSource - Interface in htsjdk.samtools.cram.ref: Interface used to supply a reference source when reading CRAM files.
CramSpanContainerIterator - Class in htsjdk.samtools.cram.build: An iterator of CRAM containers read from locations in SeekableStream.
CramVersionPolicies - Class in htsjdk.samtools.cram.common: The class provides version-dependant rules and policies for CRAM data.
CramVersionPolicies() - Constructor for class htsjdk.samtools.cram.common.CramVersionPolicies
CramVersions - Class in htsjdk.samtools.cram.common
CramVersions() - Constructor for class htsjdk.samtools.cram.common.CramVersions
CRC32 - Static variable in class htsjdk.samtools.cram.digest.ContentDigests
CRC32InputStream - Class in htsjdk.samtools.cram.io: An input stream that calculates CRC32 of all the bytes passed through it.
CRC32InputStream(InputStream) - Constructor for class htsjdk.samtools.cram.io.CRC32InputStream
CRC32OutputStream - Class in htsjdk.samtools.cram.io: An output stream that calculates CRC32 checksum of all the bytes written through the stream.
CRC32OutputStream(OutputStream) - Constructor for class htsjdk.samtools.cram.io.CRC32OutputStream
create(CramCompressionRecord) - Method in class htsjdk.samtools.cram.build.Cram2SamRecordFactory
create(EnumSet<ContentDigests.KNOWN_DIGESTS>) - Static method in class htsjdk.samtools.cram.digest.ContentDigests
create(SAMBinaryTagAndValue) - Static method in class htsjdk.samtools.cram.digest.ContentDigests
create(List<T>) - Static method in class htsjdk.samtools.util.OverlapDetector: Creates a new OverlapDetector with no trim and the given set of intervals.
create(byte[], boolean) - Static method in class htsjdk.variant.variantcontext.Allele: Create a new Allele that includes bases and if tagged as the reference allele if isRef == true.
create(byte, boolean) - Static method in class htsjdk.variant.variantcontext.Allele
create(byte) - Static method in class htsjdk.variant.variantcontext.Allele
create(String, boolean) - Static method in class htsjdk.variant.variantcontext.Allele
create(String) - Static method in class htsjdk.variant.variantcontext.Allele: Creates a non-Ref allele.
create(byte[]) - Static method in class htsjdk.variant.variantcontext.Allele: Creates a non-Ref allele.
create(Allele, boolean) - Static method in class htsjdk.variant.variantcontext.Allele: Creates a new allele based on the provided one.
create(String, List<Allele>) - Static method in class htsjdk.variant.variantcontext.GenotypeBuilder
create(String, List<Allele>, Map<String, Object>) - Static method in class htsjdk.variant.variantcontext.GenotypeBuilder
create(String, List<Allele>, double[]) - Static method in class htsjdk.variant.variantcontext.GenotypeBuilder
create() - Static method in class htsjdk.variant.variantcontext.GenotypesContext: Basic creation routine
create(int) - Static method in class htsjdk.variant.variantcontext.GenotypesContext: Basic creation routine
create(ArrayList<Genotype>, Map<String, Integer>, List<String>) - Static method in class htsjdk.variant.variantcontext.GenotypesContext: Create a fully resolved GenotypeContext containing genotypes, sample lookup table, and sorted sample names
create(ArrayList<Genotype>) - Static method in class htsjdk.variant.variantcontext.GenotypesContext: Create a fully resolved GenotypeContext containing genotypes
create(Genotype...) - Static method in class htsjdk.variant.variantcontext.GenotypesContext: Create a fully resolved GenotypeContext containing genotypes
create(File, SAMSequenceDictionary) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
create(File, SAMSequenceDictionary, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
create(File, OutputStream, SAMSequenceDictionary) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
create(OutputStream, SAMSequenceDictionary, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
create(File, OutputStream, SAMSequenceDictionary, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
create(File, OutputStream, SAMSequenceDictionary, IndexCreator, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
CREATE_INDEX - Static variable in class htsjdk.samtools.Defaults: Should BAM index files be created when writing out coordinate sorted BAM files? Default = false.
CREATE_MD5 - Static variable in class htsjdk.samtools.Defaults: Should MD5 files be created when writing out SAM and BAM files? Default = false.
createAndWriteIndex(File, File, boolean) - Static method in class htsjdk.samtools.BAMIndexer: Generates a BAM index file, either textual or binary, from an input BAI file.
createAndWriteNewIndex(File, File, FeatureCodec) - Static method in class htsjdk.tribble.example.CountRecords: creates a new index, given the feature file and the codec
createBAMRecord(SAMFileHeader, int, int, short, short, int, int, int, int, int, int, int, byte[]) - Method in class htsjdk.samtools.DefaultSAMRecordFactory: Create a new BAM Record.
createBAMRecord(SAMFileHeader, int, int, short, short, int, int, int, int, int, int, int, byte[]) - Method in interface htsjdk.samtools.SAMRecordFactory: Create a new BAM Record.
createBcf2(File, OutputStream, SAMSequenceDictionary, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
createBcf2(File, OutputStream, SAMSequenceDictionary, IndexCreator, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
createBeginRecord(SAMRecord, int, int, int) - Static method in class htsjdk.samtools.util.EdgingRecordAndOffset
createBlockCompressedVcf(File, OutputStream, SAMSequenceDictionary, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
createBlockCompressedVcf(File, OutputStream, SAMSequenceDictionary, IndexCreator, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
createBZIP2() - Static method in class htsjdk.samtools.cram.encoding.ExternalCompressor
createCramRecord(SAMRecord) - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory: Create a CramCompressionRecord.
createDynamicIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>) - Static method in class htsjdk.tribble.index.IndexFactory: Create a dynamic index with the default balancing approach
createDynamicIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>, IndexFactory.IndexBalanceApproach) - Static method in class htsjdk.tribble.index.IndexFactory: create a dynamic index, given an input file, codec, and balance approach
createEncoding(DataSeriesType, EncodingID) - Method in class htsjdk.samtools.cram.encoding.EncodingFactory: Create an encoding for the data series type and encoding id.
createEndRecord(EdgingRecordAndOffset) - Static method in class htsjdk.samtools.util.EdgingRecordAndOffset
createGenotypeMap(String, List<Allele>, String, int) - Method in class htsjdk.variant.vcf.AbstractVCFCodec: create a genotype map
createGZIP() - Static method in class htsjdk.samtools.cram.encoding.ExternalCompressor
createIndex(SamReader, File) - Static method in class htsjdk.samtools.BAMIndexer: Generates a BAM index file from an input BAM file
createIndex(SamReader, File, Log) - Static method in class htsjdk.samtools.BAMIndexer: Generates a BAM index file from an input BAM file
createIndex(SeekableStream, File, Log, ValidationStringency) - Static method in class htsjdk.samtools.CRAMBAIIndexer: Generates a BAI index file from an input CRAM stream
createIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>, IndexFactory.IndexType) - Static method in class htsjdk.tribble.index.IndexFactory: Create a index of the specified type with default binning parameters
createIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>, IndexFactory.IndexType, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory: Create an index of the specified type with default binning parameters
createIntervalIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>) - Static method in class htsjdk.tribble.index.IndexFactory: create an interval-tree index with the default features per bin count
createIntervalIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>, int) - Static method in class htsjdk.tribble.index.IndexFactory: a helper method for creating an interval-tree index
createLinearIndex(File, FeatureCodec) - Static method in class htsjdk.tribble.index.IndexFactory: a helper method for creating a linear binned index with default bin size
createLinearIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>, int) - Static method in class htsjdk.tribble.index.IndexFactory: a helper method for creating a linear binned index
createLZMA() - Static method in class htsjdk.samtools.cram.encoding.ExternalCompressor
createMissing(String, int) - Static method in class htsjdk.variant.variantcontext.GenotypeBuilder: Create a new Genotype object for a sample that's missing from the VC (i.e., in the output header).
createProgramRecord() - Method in class htsjdk.samtools.SAMFileHeader
createRANS(RANS.ORDER) - Static method in class htsjdk.samtools.cram.encoding.ExternalCompressor
createRAW() - Static method in class htsjdk.samtools.cram.encoding.ExternalCompressor
createSAMRecord(SAMFileHeader) - Method in class htsjdk.samtools.DefaultSAMRecordFactory: Create a new SAMRecord to be filled in
createSAMRecord(SAMFileHeader) - Method in interface htsjdk.samtools.SAMRecordFactory: Create a new SAMRecord to be filled in
createSAMTag() - Method in class htsjdk.samtools.cram.structure.ReadTag
createTabixIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>, TabixFormat, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory
createTabixIndex(File, FeatureCodec<FEATURE_TYPE, SOURCE_TYPE>, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory
createTempDir(String, String) - Static method in class htsjdk.samtools.util.IOUtil: Create a temporary subdirectory in the default temporary-file directory, using the given prefix and suffix to generate the name.
createVcf(File, OutputStream, SAMSequenceDictionary, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
createVcf(File, OutputStream, SAMSequenceDictionary, IndexCreator, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory: Deprecated.
CS - Variable in class htsjdk.samtools.SAMTagUtil
CURRENT_VERSION - Static variable in class htsjdk.samtools.SAMFileHeader
CUSTOM_READER_FACTORY - Static variable in class htsjdk.samtools.Defaults: Custom reader factory able to handle URL based resources like ga4gh.
CustomGzipOutputStream - Class in htsjdk.samtools.util: Hacky little class used to allow us to set the compression level on a GZIP output stream which, for some bizarre reason, is not exposed in the standard API.
CustomReaderFactory - Class in htsjdk.samtools: Factory for creating custom readers for accessing API based resources, e.g.
CustomReaderFactory.ICustomReaderFactory - Interface in htsjdk.samtools: Interface to be implemented by custom factory classes that register themselves with this factory and are loaded dynamically.





D

DataReader<T> - Interface in htsjdk.samtools.cram.encoding.reader

A basic interface for reading data.

DataReaderFactory - Class in htsjdk.samtools.cram.encoding.reader
 
DataReaderFactory() - Constructor for class htsjdk.samtools.cram.encoding.reader.DataReaderFactory
 
DataReaderFactory.DataReaderWithStats<T> - Class in htsjdk.samtools.cram.encoding.reader
 
DataReaderWithStats(DataReader<T>) - Constructor for class htsjdk.samtools.cram.encoding.reader.DataReaderFactory.DataReaderWithStats
 
DataSeries - Annotation Type in htsjdk.samtools.cram.encoding

An annotation to denote a data series field in a java class.

DataSeriesMap - Annotation Type in htsjdk.samtools.cram.encoding
 
DataSeriesType - Enum in htsjdk.samtools.cram.encoding

Data series types known to CRAM.

DataWriter<T> - Interface in htsjdk.samtools.cram.encoding.writer

A basic interface defining a writer.

DataWriterFactory - Class in htsjdk.samtools.cram.encoding.writer
 
DataWriterFactory() - Constructor for class htsjdk.samtools.cram.encoding.writer.DataWriterFactory
 
DATE_RUN_PRODUCED_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
DateParser - Class in htsjdk.samtools.util

NOTE: This code has been taken from w3.org, and modified slightly to handle timezones of the form [-+]DDDD,
 and also to fix a bug in the application of time zone to the parsed date.

DateParser() - Constructor for class htsjdk.samtools.util.DateParser
 
DateParser.InvalidDateException - Exception in htsjdk.samtools.util
 
DBSNP_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
debug(Throwable, Object...) - Method in class htsjdk.samtools.util.Log

Logs a Throwable and optional message parts at level debug.

debug(Object...) - Method in class htsjdk.samtools.util.Log

Logs one or more message parts at level debug.

DEBUG_MODE_ENABLED - Static variable in class htsjdk.variant.utils.GeneralUtils

Setting this to true causes the VCF/BCF/VariantContext classes to emit debugging information
 to standard error

debugGetTree(String) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
DECIMAL_DIGITS_TO_PRINT - Static variable in class htsjdk.samtools.util.FormatUtil
 
decode() - Method in class htsjdk.samtools.BAMRecordCodec

Read the next record from the input stream and convert into a java object.

decode() - Method in interface htsjdk.samtools.CoordinateSortedPairInfoMap.Codec

Read the next key and record from the input stream and convert into a java object.

decode(LineReader, String) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec

Reads text SAM header and converts to a SAMSequenceDictionary object.

decode(LineReader, String) - Method in class htsjdk.samtools.SAMTextHeaderCodec

Reads text SAM header and converts to a SAMFileHeader object.

decode(String) - Static method in class htsjdk.samtools.TextCigarCodec

Convert from String CIGAR representation to Cigar class representation.

decode(String) - Method in class htsjdk.samtools.TextTagCodec

Convert typed tag in SAM text format (name:type:value) into tag name and Object value representation.

decode() - Method in interface htsjdk.samtools.util.SortingCollection.Codec

Read the next record from the input stream and convert into a java object.

decode(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec

Convenience method.

decode(String) - Method in class htsjdk.tribble.AsciiFeatureCodec
 
decode(String) - Method in class htsjdk.tribble.bed.BEDCodec
 
decode(String[]) - Method in class htsjdk.tribble.bed.BEDCodec
 
decode(PositionalBufferedStream) - Method in class htsjdk.tribble.example.ExampleBinaryCodec
 
decode(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec

Decode a single Feature from the SOURCE, reading no further in the underlying source than beyond that feature.

decode(String) - Method in class htsjdk.tribble.gelitext.GeliTextCodec

Deprecated.
 
decode(String[]) - Method in class htsjdk.tribble.gelitext.GeliTextCodec

Deprecated.
 
decode(PositionalBufferedStream) - Method in class htsjdk.variant.bcf2.BCF2Codec
 
decode(List<Allele>, String, BCF2Decoder, byte, int, GenotypeBuilder[]) - Method in interface htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders.Decoder
 
decode() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext

Force us to decode the genotypes, if not already done

decode(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec

decode the line into a feature (VariantContext)

decode() - Method in class htsjdk.variant.vcf.VCFRecordCodec
 
decodeInt(byte, int) - Method in class htsjdk.variant.bcf2.BCF2Decoder

Decode an int from the stream.

decodeInt(BCF2Type) - Method in class htsjdk.variant.bcf2.BCF2Decoder
 
decodeIntArray(int, BCF2Type, int[]) - Method in class htsjdk.variant.bcf2.BCF2Decoder

Low-level reader for int[]

 Requires a typeDescriptor so the function knows how many elements to read,
 and how they are encoded.

decodeIntArray(byte, int) - Method in class htsjdk.variant.bcf2.BCF2Decoder
 
decodeLoc(SOURCE) - Method in class htsjdk.tribble.AbstractFeatureCodec
 
decodeLoc(String) - Method in class htsjdk.tribble.bed.BEDCodec
 
decodeLoc(PositionalBufferedStream) - Method in class htsjdk.tribble.example.ExampleBinaryCodec
 
decodeLoc(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec

Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.

decodeLoc(String) - Method in class htsjdk.tribble.gelitext.GeliTextCodec

Deprecated.
 
decodeLoc(PositionalBufferedStream) - Method in class htsjdk.variant.bcf2.BCF2Codec
 
decodeLoc(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec

the fast decode function

decodeNumberOfElements(byte) - Method in class htsjdk.variant.bcf2.BCF2Decoder
 
decodeSingleValue(BCF2Type) - Method in class htsjdk.variant.bcf2.BCF2Decoder
 
decodeSize(byte) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
decodeType(byte) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
decodeTypedValue() - Method in class htsjdk.variant.bcf2.BCF2Decoder
 
decodeTypedValue(byte) - Method in class htsjdk.variant.bcf2.BCF2Decoder
 
decodeTypedValue(byte, int) - Method in class htsjdk.variant.bcf2.BCF2Decoder
 
decodeTypeID(byte) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
deepCopy() - Method in class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue

Creates and returns a deep copy of the list of tag/values.

deepCopy() - Method in class htsjdk.samtools.SAMBinaryTagAndValue

Creates and returns a deep copy of the list of tag/values.

deepCopy() - Method in class htsjdk.samtools.SAMRecord

Returns a deep copy of the SAM record, with the following exceptions:

  - The header field, which shares the header reference with the original record
  - The file source field, which will always always be set to null in the copy

DEFAULT_BIN_WIDTH - Static variable in class htsjdk.tribble.index.linear.LinearIndexCreator
 
DEFAULT_BUFFER_SIZE - Static variable in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
DEFAULT_CHROMOSOME_LENGTH - Static variable in class htsjdk.samtools.SAMRecordSetBuilder
 
DEFAULT_COMPRESSION_LEVEL - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
DEFAULT_CRAM_VERSION - Static variable in class htsjdk.samtools.cram.common.CramVersions

The default CRAM version when creating a new CRAM output file or stream.

DEFAULT_DICTIONARY_EQUAL_TAG - Static variable in class htsjdk.samtools.SAMSequenceDictionary
 
DEFAULT_DUPLICATE_SCORING_STRATEGY - Static variable in class htsjdk.samtools.SAMRecordSetBuilder
 
DEFAULT_FEATURE_COUNT - Static variable in class htsjdk.tribble.index.interval.IntervalIndexCreator
 
DEFAULT_HEADER_KEY - Static variable in class htsjdk.samtools.filter.AbstractJavascriptFilter
 
DEFAULT_LIFTOVER_MINMATCH - Static variable in class htsjdk.samtools.liftover.LiftOver
 
DEFAULT_MAX_RECORDS_TO_ITERATE - Static variable in class htsjdk.samtools.util.QualityEncodingDetector

The maximum number of records over which the detector will iterate before making a determination, by default.

DEFAULT_OPTIONS - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
 
DEFAULT_OPTIONS - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.
 
DEFAULT_QUEUE_SIZE - Static variable in class htsjdk.samtools.util.AbstractAsyncWriter
 
DEFAULT_STRINGENCY - Static variable in enum htsjdk.samtools.ValidationStringency
 
DEFAULT_UNCOMPRESSED_BLOCK_SIZE - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
DEFAULT_WINDOW_SIZE - Static variable in class htsjdk.samtools.cram.ref.ReferenceTracks
 
defaultBinSize() - Method in class htsjdk.tribble.index.linear.LinearIndexCreator

the current default bin size

DefaultBitInputStream - Class in htsjdk.samtools.cram.io

Must not read from delegate unless no bits left in the buffer!!!

DefaultBitInputStream(InputStream) - Constructor for class htsjdk.samtools.cram.io.DefaultBitInputStream
 
DefaultBitOutputStream - Class in htsjdk.samtools.cram.io
 
DefaultBitOutputStream(OutputStream) - Constructor for class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
DefaultingMap(V) - Constructor for class htsjdk.samtools.util.CollectionUtil.DefaultingMap

Creates a defaulting map which defaults to the provided value and with injecting-on-default disabled.

DefaultingMap(CollectionUtil.DefaultingMap.Factory<V, K>, boolean) - Constructor for class htsjdk.samtools.util.CollectionUtil.DefaultingMap

Creates a defaulting map that generates defaults from the provided factory.

Defaults - Class in htsjdk.samtools

Embodies defaults for global values that affect how the SAM JDK operates.

Defaults() - Constructor for class htsjdk.samtools.Defaults
 
DEFAULTS - Static variable in enum htsjdk.samtools.SamReaderFactory.Option
 
DefaultSAMRecordFactory - Class in htsjdk.samtools

Default factory for creating SAM and BAM records used by the SamReader classes.

DefaultSAMRecordFactory() - Constructor for class htsjdk.samtools.DefaultSAMRecordFactory
 
DeflaterFactory - Class in htsjdk.samtools.util.zip

Factory for Deflater objects used by BlockCompressedOutputStream.

DeflaterFactory() - Constructor for class htsjdk.samtools.util.zip.DeflaterFactory
 
DelegatingIterator<T> - Class in htsjdk.samtools.util

Simple iterator class that delegates all method calls to an underlying iterator.

DelegatingIterator(Iterator<T>) - Constructor for class htsjdk.samtools.util.DelegatingIterator
 
deleteDirectoryTree(File) - Static method in class htsjdk.samtools.util.IOUtil

Delete the given file or directory.

deleteFiles(File...) - Static method in class htsjdk.samtools.util.IOUtil

Delete a list of files, and write a warning message if one could not be deleted.

deleteFiles(Iterable<File>) - Static method in class htsjdk.samtools.util.IOUtil
 
DELETION - Static variable in enum htsjdk.samtools.CigarOperator
 
Deletion - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing a deletion of one or more bases similar to CigarOperator.D.

Deletion() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
Deletion(int, int) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
DELETION_ALLELE_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
deletionLengthCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
deletionLengthCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
DEPTH_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
deriveTypeFromKeyAndType(String, Object) - Static method in class htsjdk.samtools.cram.structure.ReadTag
 
deriveTypeFromValue(String, Object) - Static method in class htsjdk.samtools.cram.structure.ReadTag
 
description - Variable in enum htsjdk.samtools.DownsamplingIteratorFactory.Strategy
 
DESCRIPTION_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
detachedCount - Static variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
detachFromIterator() - Method in class htsjdk.samtools.sra.SRALazyRecord

Is being called when original NGS iterator is being moved to the next object.

detect(long, FastqReader...) - Static method in class htsjdk.samtools.util.QualityEncodingDetector

Reads through the records in the provided fastq reader and uses their quality scores to determine the quality
 format used in the fastq.

detect(FastqReader...) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
 
detect(long, CloseableIterator<SAMRecord>, boolean) - Static method in class htsjdk.samtools.util.QualityEncodingDetector

Reads through the records in the provided SAM reader and uses their quality scores to determine the quality
 format used in the SAM.

detect(long, CloseableIterator<SAMRecord>) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
 
detect(long, SamReader) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
 
detect(SamReader) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
 
detect(SamReader, FastqQualityFormat) - Static method in class htsjdk.samtools.util.QualityEncodingDetector

Reads through the records in the provided SAM reader and uses their quality scores to sanity check the expected
 quality passed in.

determineIntegerType(int) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
determineIntegerType(int[]) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
determineIntegerType(List<Integer>) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
determineOutputTypeFromFile(File) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Attempts to determine the type of file/data to write based on the File path being
 written to.

determineType() - Method in class htsjdk.variant.variantcontext.Genotype

Internal code to determine the type of the genotype from the alleles vector

diagnosticLiftover(Interval) - Method in class htsjdk.samtools.liftover.LiftOver
 
DICT_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
 
dictionary - Variable in class htsjdk.samtools.cram.structure.CompressionHeader
 
difference(Collection<IntervalList>, Collection<IntervalList>) - Static method in class htsjdk.samtools.util.IntervalList

A utility function for finding the difference between two IntervalLists.

DiploidGenotype - Enum in htsjdk.tribble.gelitext

Deprecated.

disable(SamReaderFactory.Option...) - Method in class htsjdk.samtools.SamReaderFactory

Disables the provided SamReaderFactory.Options, then returns itself.

disableOnTheFlyModifications() - Method in class htsjdk.variant.vcf.AbstractVCFCodec

Forces all VCFCodecs to not perform any on the fly modifications to the VCF header
 of VCF records.

disconnect() - Method in class htsjdk.samtools.util.ftp.FTPClient

Disconnects from the host to which we are currently connected.

DiskBackedQueue<E> - Class in htsjdk.samtools.util

A single-ended FIFO queue.

DiskBasedBAMFileIndex - Class in htsjdk.samtools

A class for reading BAM file indices, hitting the disk once per query.

DiskBasedBAMFileIndex(File, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.DiskBasedBAMFileIndex
 
DiskBasedBAMFileIndex(SeekableStream, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.DiskBasedBAMFileIndex
 
DiskBasedBAMFileIndex(File, SAMSequenceDictionary, boolean) - Constructor for class htsjdk.samtools.DiskBasedBAMFileIndex
 
distanceC - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
distanceToNextFragmentCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
divideByHistogram(Histogram<K>) - Method in class htsjdk.samtools.util.Histogram

Immutable method that divides the current Histogram by an input Histogram and generates a new one
 Throws an exception if the bins don't match up exactly

done(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
 
doneAdding() - Method in class htsjdk.samtools.util.SortingCollection

This method can be called after caller is done adding to collection, in order to possibly free
 up memory.

doneAddingStartIteration() - Method in class htsjdk.samtools.util.SortingLongCollection

This method must be called after done adding, and before calling hasNext() or next().

doOnTheFlyModifications - Variable in class htsjdk.variant.vcf.AbstractVCFCodec

If true, then we'll magically fix up VCF headers on the fly when we read them in

DownsamplingIterator - Class in htsjdk.samtools

Abstract base class for all DownsamplingIterators that provides a uniform interface for recording
 and reporting statistics bout how many records have been kept and discarded.

DownsamplingIterator(double) - Constructor for class htsjdk.samtools.DownsamplingIterator

Constructs a downsampling iterator that aims to retain the targetProportion of reads.

DownsamplingIteratorFactory - Class in htsjdk.samtools

A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while
 meeting various criteria.

DownsamplingIteratorFactory() - Constructor for class htsjdk.samtools.DownsamplingIteratorFactory
 
DownsamplingIteratorFactory.Strategy - Enum in htsjdk.samtools

Describes the available downsampling strategies.

DP(int) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

This genotype has this DP value

DPAccessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.DPAccessor
 
drop() - Static method in class htsjdk.samtools.cram.lossy.QualityScoreTreatment
 
DUPLICATE_READ_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
DuplicateReadFilter - Class in htsjdk.samtools.filter

Filter out SAMRecords with DuplicateRead flag set

 $Id$

DuplicateReadFilter() - Constructor for class htsjdk.samtools.filter.DuplicateReadFilter
 
DuplicateScoringStrategy - Class in htsjdk.samtools

This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate
 during duplicate marking (see MarkDuplicates).

DuplicateScoringStrategy() - Constructor for class htsjdk.samtools.DuplicateScoringStrategy
 
DuplicateScoringStrategy.ScoringStrategy - Enum in htsjdk.samtools
 
DuplicateSet - Class in htsjdk.samtools

Stores a set of records that are duplicates of each other.

DuplicateSet() - Constructor for class htsjdk.samtools.DuplicateSet

Sets the duplicate flag by default

DuplicateSet(boolean) - Constructor for class htsjdk.samtools.DuplicateSet
 
DuplicateSet(SAMRecordDuplicateComparator) - Constructor for class htsjdk.samtools.DuplicateSet
 
DuplicateSet(boolean, SAMRecordDuplicateComparator) - Constructor for class htsjdk.samtools.DuplicateSet
 
duplicateSetCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordDuplicateComparator

Less stringent than compare, such that two records are equal enough such that their ordering within their duplicate set would be arbitrary.

DuplicateSetIterator - Class in htsjdk.samtools

An iterator of sets of duplicates.

DuplicateSetIterator(CloseableIterator<SAMRecord>, SAMFileHeader) - Constructor for class htsjdk.samtools.DuplicateSetIterator
 
DuplicateSetIterator(CloseableIterator<SAMRecord>, SAMFileHeader, boolean) - Constructor for class htsjdk.samtools.DuplicateSetIterator
 
DuplicateSetIterator(CloseableIterator<SAMRecord>, SAMFileHeader, boolean, SAMRecordDuplicateComparator) - Constructor for class htsjdk.samtools.DuplicateSetIterator
 
DuplicateSetIterator(CloseableIterator<SAMRecord>, SAMFileHeader, boolean, SAMRecordDuplicateComparator, Log) - Constructor for class htsjdk.samtools.DuplicateSetIterator

Allows the user of this iterator to skip the sorting of the input if the input is already sorted.

DynamicIndexCreator - Class in htsjdk.tribble.index

A DynamicIndexCreator creates the proper index based on an IndexFactory.IndexBalanceApproach and
 the characteristics of the file.

DynamicIndexCreator(File, IndexFactory.IndexBalanceApproach) - Constructor for class htsjdk.tribble.index.DynamicIndexCreator
 




E

E2 - Variable in class htsjdk.samtools.SAMTagUtil
 
eagerDecode() - Method in class htsjdk.samtools.BAMRecord

Force all the lazily-initialized attributes to be decoded.

eagerDecode() - Method in class htsjdk.samtools.SAMRecord

Force all lazily-initialized data members to be initialized.

EBI_REFERENCE_SERVICE_URL_MASK - Static variable in class htsjdk.samtools.Defaults

A mask (pattern) to use when building EBI reference service URL for a
 given MD5 checksum.

EdgeReadIterator - Class in htsjdk.samtools.util

Iterator that traverses a SAM File, accumulating information on a per-locus basis.

EdgeReadIterator(SamReader) - Constructor for class htsjdk.samtools.util.EdgeReadIterator

Prepare to iterate through the given SAM records, skipping non-primary alignments.

EdgeReadIterator(SamReader, IntervalList) - Constructor for class htsjdk.samtools.util.EdgeReadIterator

Prepare to iterate through the given SAM records, skipping non-primary alignments.

EdgeReadIterator(SamReader, IntervalList, boolean) - Constructor for class htsjdk.samtools.util.EdgeReadIterator

Prepare to iterate through the given SAM records, skipping non-primary alignments

EdgingRecordAndOffset - Class in htsjdk.samtools.util

Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds
 to the base and quality for the start of alignment block at the genomic position described by the AbstractLocusInfo.

EdgingRecordAndOffset.Type - Enum in htsjdk.samtools.util

Describes the type of TypedRecordAndOffset, whether it represents the start or the end of
 an alignment block.

element() - Method in class htsjdk.samtools.util.DiskBackedQueue
 
embeddedRefBlock - Variable in class htsjdk.samtools.cram.structure.Slice
 
embeddedRefBlockContentID - Variable in class htsjdk.samtools.cram.structure.Slice
 
EMPTY_ALLELE - Static variable in class htsjdk.variant.vcf.VCFConstants
 
EMPTY_ALTERNATE_ALLELE_FIELD - Static variable in class htsjdk.variant.vcf.VCFConstants
 
EMPTY_GENOTYPE - Static variable in class htsjdk.variant.vcf.VCFConstants
 
EMPTY_GZIP_BLOCK - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
EMPTY_HEADER - Static variable in class htsjdk.tribble.FeatureCodecHeader

An public instance representing no header

EMPTY_ID_FIELD - Static variable in class htsjdk.variant.vcf.VCFConstants
 
EMPTY_INFO_FIELD - Static variable in class htsjdk.variant.vcf.VCFConstants
 
EMPTY_STRING - Static variable in class htsjdk.samtools.util.StringUtil

Returns Object.toString() of the provided value if it isn't null; "" otherwise.

emptyID() - Method in class htsjdk.variant.variantcontext.VariantContext
 
enable(SamReaderFactory.Option...) - Method in class htsjdk.samtools.SamReaderFactory

Enables the provided SamReaderFactory.Options, then returns itself.

enableAdaptiveIndexing - Static variable in class htsjdk.tribble.index.linear.LinearIndex
 
EnaRefService - Class in htsjdk.samtools.cram.ref
 
EnaRefService() - Constructor for class htsjdk.samtools.cram.ref.EnaRefService
 
EnaRefService.GaveUpException - Exception in htsjdk.samtools.cram.ref
 
encloses(int, int, int, int) - Static method in class htsjdk.samtools.util.CoordMath

Returns true if the "inner" coords and totally enclosed by the "outer" coords.

encode(SAMRecord) - Method in class htsjdk.samtools.BAMRecordCodec

Write object to OutputStream.

encode(KEY, REC) - Method in interface htsjdk.samtools.CoordinateSortedPairInfoMap.Codec

Write object to output stream.

encode(SAMSequenceDictionary) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec

Convert SAMSequenceDictionary from in-memory representation to text representation.

encode(Writer, SAMFileHeader) - Method in class htsjdk.samtools.SAMTextHeaderCodec

Convert SAMFileHeader from in-memory representation to text representation.

encode(Writer, SAMFileHeader, boolean) - Method in class htsjdk.samtools.SAMTextHeaderCodec

Convert SAMFileHeader from in-memory representation to text representation.

encode(Cigar) - Static method in class htsjdk.samtools.TextCigarCodec

Convert from Cigar class representation to String.

encode(String, Object) - Method in class htsjdk.samtools.TextTagCodec

Convert in-memory representation of tag to SAM text representation.

encode(T) - Method in interface htsjdk.samtools.util.SortingCollection.Codec

Write object to output stream

encode(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder

Totally generic encoder that examines o, determines the best way to encode it, and encodes it

 This method is incredibly slow, but it's only used for UnitTests so it doesn't matter

encode(VariantContext) - Method in class htsjdk.variant.vcf.VCFEncoder
 
encode(VariantContext) - Method in class htsjdk.variant.vcf.VCFRecordCodec
 
encodeHeaderLine(boolean) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec

Write Header line.

encodeRawBytes(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeRawChar(byte) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeRawFloat(double) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeRawInt(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeRawMissingValue(BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeRawMissingValues(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeRawString(String, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeRawValue(T, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeRawValues(Collection<T>, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeSequenceRecord(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec

Write SAMSequenceRecord.

encodeType(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeTyped(Object, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeTyped(List<? extends Object>, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeTypeDescriptor(int, BCF2Type) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
encodeTypedFloat(double) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeTypedInt(int) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeTypedInt(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeTypedMissing(BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeTypedString(String) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeTypedString(byte[]) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
encodeUntypedTag(String, Object) - Method in class htsjdk.samtools.TextTagCodec

Encode a standard header tag, which should not have a type field.

encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.AtomicInt
 
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

Key abstract method that should encode a value of the given type into the encoder.

encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Flag
 
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Float
 
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.GenericInts
 
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
 
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
 
Encoding<T> - Interface in htsjdk.samtools.cram.encoding

An interface to describe how a data series is encoded.

EncodingFactory - Class in htsjdk.samtools.cram.encoding

A helper class to instantiate an appropriate Encoding
 for a given DataSeriesType and
 Encoding.

EncodingFactory() - Constructor for class htsjdk.samtools.cram.encoding.EncodingFactory
 
EncodingID - Enum in htsjdk.samtools.cram.structure

Encoding ID as defined in the CRAM specs.

EncodingKey - Enum in htsjdk.samtools.cram.structure
 
encodingMap - Variable in class htsjdk.samtools.cram.structure.CompressionHeader
 
EncodingParams - Class in htsjdk.samtools.cram.structure
 
EncodingParams(EncodingID, byte[]) - Constructor for class htsjdk.samtools.cram.structure.EncodingParams
 
end - Variable in class htsjdk.samtools.QueryInterval

1-based, inclusive.

end - Variable in class htsjdk.tribble.bed.SimpleBEDFeature
 
end - Variable in class htsjdk.tribble.util.TabixUtils.TIntv
 
END_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
endOfBlock() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
 
endPositionColumn - Variable in class htsjdk.tribble.index.tabix.TabixFormat

One-based index of the column in the file being indexed containing the end position.

engine - Static variable in class htsjdk.variant.variantcontext.VariantContextUtils

Use a Lazy JexlEngine instance to avoid class-loading issues.

ensure(int, int) - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
 
ensureRange(int, int) - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
 
ensureSampleNameMap() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
ensureSampleNameMap() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext

Overrides the ensure* functionality.

ensureSampleOrdering() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
ensureSampleOrdering() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
 
entrySet() - Method in class htsjdk.samtools.util.IntervalTreeMap
 
enumToBinary(CigarOperator) - Static method in enum htsjdk.samtools.CigarOperator
 
enumToCharacter(CigarOperator) - Static method in enum htsjdk.samtools.CigarOperator

Returns the character that should be used within a SAM file.

eof() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
 
eof() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
eof() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
eof() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
eof() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
 
eof() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
eof() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
 
eof() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
 
eof() - Method in class htsjdk.samtools.seekablestream.SeekableStream
 
eof() - Method in class htsjdk.samtools.util.FastLineReader
 
eofNotFound(Version) - Static method in class htsjdk.samtools.cram.common.CramVersionPolicies

The method holds the behaviour for when the EOF marker is not found.

equals(Object) - Method in class htsjdk.samtools.Bin

See whether two bins are equal.

equals(Object) - Method in class htsjdk.samtools.BinningIndexContent.BinList
 
equals(Object) - Method in class htsjdk.samtools.BinningIndexContent
 
equals(Object) - Method in class htsjdk.samtools.Chunk
 
equals(Object) - Method in class htsjdk.samtools.Cigar
 
equals(Object) - Method in class htsjdk.samtools.CigarElement
 
equals(Object) - Method in class htsjdk.samtools.cram.common.Version

Check if another version is exactly the same as this one.

equals(Object) - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
equals(Object) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
equals(Object) - Method in class htsjdk.samtools.cram.structure.CramHeader

Checks if content of a header is the same as this one.

equals(Object) - Method in class htsjdk.samtools.cram.structure.ReadTag
 
equals(Object) - Method in class htsjdk.samtools.fastq.FastqRecord
 
equals(Object) - Method in class htsjdk.samtools.LinearIndex
 
equals(Object) - Method in class htsjdk.samtools.metrics.MetricBase

An equals method that checks equality by asserting that the classes are of the exact
 same type and that all public fields are equivalent.

equals(Object) - Method in class htsjdk.samtools.metrics.MetricsFile

Checks that the headers, metrics and histogram are all equal.

equals(Object) - Method in class htsjdk.samtools.metrics.StringHeader

Checks equality on the value of the header.

equals(Object) - Method in class htsjdk.samtools.metrics.VersionHeader

Equals method that checks that both the item and version string are equal.

equals(Object) - Method in class htsjdk.samtools.reference.FastaSequenceIndex

Compare two FastaSequenceIndex objects for equality.

equals(Object) - Method in class htsjdk.samtools.SAMBinaryTagAndValue
 
equals(Object) - Method in class htsjdk.samtools.SAMFileHeader
 
equals(Object) - Method in class htsjdk.samtools.SAMProgramRecord
 
equals(Object) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
equals(Object) - Method in class htsjdk.samtools.SAMRecord
 
equals(Object) - Method in class htsjdk.samtools.SAMSequenceDictionary

returns true if the two dictionaries are the same, aliases are NOT considered

equals(Object) - Method in class htsjdk.samtools.SAMSequenceRecord
 
equals(Object) - Method in class htsjdk.samtools.sra.SRALazyRecord

For records equality, we should only compare read id, reference and position on the reference.

equals(Object) - Method in class htsjdk.samtools.util.Histogram.Bin

Checks the equality of the bin by ID and value.

equals(Object) - Method in class htsjdk.samtools.util.Histogram

Checks that the labels and values in the two histograms are identical.

equals(Object) - Method in class htsjdk.samtools.util.Interval

Equals method that agrees with Interval.compareTo(Interval).

equals(Object) - Method in class htsjdk.samtools.util.IntervalList
 
equals(Object) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
equals(Object) - Method in class htsjdk.samtools.util.RelativeIso8601Date
 
equals(Object) - Method in class htsjdk.samtools.util.Tuple
 
equals(Object) - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
equals(Object) - Method in class htsjdk.tribble.index.Block
 
equals(Object) - Method in class htsjdk.tribble.index.interval.Interval
 
equals(Object) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
equals(Object) - Method in class htsjdk.tribble.index.tabix.TabixFormat
 
equals(Object) - Method in class htsjdk.tribble.index.tabix.TabixIndex
 
equals(Object) - Method in class htsjdk.variant.variantcontext.Allele
 
equals(Allele, boolean) - Method in class htsjdk.variant.variantcontext.Allele

Returns true if this and other are equal.

equals(Object) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
equals(Object) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine

returns true if we're equal to another compound header line

equals(Object) - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
 
equals(Object) - Method in class htsjdk.variant.vcf.VCFHeaderLine
 
equals(Object) - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
 
equalsExcludingDescription(VCFCompoundHeaderLine) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
equalsIgnoreProperties(Object) - Method in class htsjdk.tribble.index.AbstractIndex
 
equalsIgnoreProperties(Object) - Method in interface htsjdk.tribble.index.Index

Returns true if this and obj are 'effectively' equivalent indices.

equalsIgnoreProperties(Object) - Method in class htsjdk.tribble.index.tabix.TabixIndex
 
equivalent(SAMProgramRecord) - Method in class htsjdk.samtools.SAMProgramRecord
 
equivalent(SAMReadGroupRecord) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
error(Throwable, Object...) - Method in class htsjdk.samtools.util.Log

Logs a Throwable and optional message parts at level error.

error(Object...) - Method in class htsjdk.samtools.util.Log

Logs one or more message parts at level error.

estimateSdViaMad() - Method in class htsjdk.samtools.util.Histogram

Returns a value that is intended to estimate the mean of the distribution, if the distribution is
 essentially normal, by using the median absolute deviation to remove the effect of
 erroneous massive outliers.

ExampleBinaryCodec - Class in htsjdk.tribble.example

An example binary codec that encodes / decodes contig / start / stop values via DataInputStreams

ExampleBinaryCodec() - Constructor for class htsjdk.tribble.example.ExampleBinaryCodec
 
ExampleSamUsage - Class in htsjdk.samtools.example
 
ExampleSamUsage() - Constructor for class htsjdk.samtools.example.ExampleSamUsage
 
EXCLUDE_INTERVALS_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
 
execute(String) - Static method in class htsjdk.samtools.util.ProcessExecutor

Executes the command via Runtime.getRuntime().exec() then writes stderr to log.error
 and stdout to log.info and blocks until the command is complete.

execute(String[]) - Static method in class htsjdk.samtools.util.ProcessExecutor

Executes the command via Runtime.getRuntime().exec() then writes stderr to log.error
 and stdout to log.info and blocks until the command is complete.

execute(String[], String) - Static method in class htsjdk.samtools.util.ProcessExecutor

Executes the command via Runtime.getRuntime().exec(), writes outputStreamString
 to the process output stream if it is not null, then writes stderr to log.error
 and stdout to log.info and blocks until the command is complete.

executeAndReturnInterleavedOutput(String) - Static method in class htsjdk.samtools.util.ProcessExecutor

Execute the command and capture stdout and stderr.

executeAndReturnInterleavedOutput(String[]) - Static method in class htsjdk.samtools.util.ProcessExecutor

Execute the command and capture stdout and stderr.

executeAndReturnResult(String) - Static method in class htsjdk.samtools.util.ProcessExecutor
 
executeCommand(String) - Method in class htsjdk.samtools.util.ftp.FTPClient

Executes the given FTP command on our current connection, returning the
 three digit response code from the server.

exhaustivelyTestIndex(SamReader) - Static method in class htsjdk.samtools.BamIndexValidator
 
exists() - Method in class htsjdk.tribble.util.FTPHelper
 
exists() - Method in class htsjdk.tribble.util.HTTPHelper
 
exists() - Method in class htsjdk.tribble.util.RemoteURLHelper
 
exists() - Method in interface htsjdk.tribble.util.URLHelper
 
exitStatus - Variable in class htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
 
ExitStatusAndOutput(int, String, String) - Constructor for class htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
 
Exon(int, int) - Constructor for class htsjdk.tribble.bed.FullBEDFeature.Exon

Constructs ...

Exon2(int, int, int, int) - Constructor for class htsjdk.tribble.bed.FullBEDFeature.Exon2
 
exp - Variable in class htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
 
EXPECTED_ALLELE_COUNT_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
explodeStringList(String) - Static method in class htsjdk.variant.bcf2.BCF2Utils

Inverse operation of collapseStringList.

ExposedByteArrayOutputStream - Class in htsjdk.samtools.cram.io
 
ExposedByteArrayOutputStream() - Constructor for class htsjdk.samtools.cram.io.ExposedByteArrayOutputStream
 
extend(Allele, byte[]) - Static method in class htsjdk.variant.variantcontext.Allele
 
external - Variable in class htsjdk.samtools.cram.structure.Slice
 
ExternalByteArrayEncoding - Class in htsjdk.samtools.cram.encoding
 
ExternalByteArrayEncoding() - Constructor for class htsjdk.samtools.cram.encoding.ExternalByteArrayEncoding
 
ExternalByteEncoding - Class in htsjdk.samtools.cram.encoding
 
ExternalByteEncoding() - Constructor for class htsjdk.samtools.cram.encoding.ExternalByteEncoding
 
ExternalCompression - Class in htsjdk.samtools.cram.io

Methods to provide CRAM external compression/decompression features.

ExternalCompression() - Constructor for class htsjdk.samtools.cram.io.ExternalCompression
 
ExternalCompressor - Class in htsjdk.samtools.cram.encoding
 
externalCompressors - Variable in class htsjdk.samtools.cram.structure.CompressionHeader
 
externalIds - Variable in class htsjdk.samtools.cram.structure.CompressionHeader
 
ExternalIntegerEncoding - Class in htsjdk.samtools.cram.encoding
 
ExternalIntegerEncoding() - Constructor for class htsjdk.samtools.cram.encoding.ExternalIntegerEncoding
 
ExternalLongEncoding - Class in htsjdk.samtools.cram.encoding
 
ExternalLongEncoding() - Constructor for class htsjdk.samtools.cram.encoding.ExternalLongEncoding
 
extractDictionary(File) - Static method in class htsjdk.variant.utils.SAMSequenceDictionaryExtractor
 
extraStrictValidation(Allele, Allele, Set<String>) - Method in class htsjdk.variant.variantcontext.VariantContext

Run all extra-strict validation tests on a Variant Context object





F

FailsVendorReadQualityFilter - Class in htsjdk.samtools.filter

Filter for filtering out reads that do not pass the quality filter

 $Id$

FailsVendorReadQualityFilter() - Constructor for class htsjdk.samtools.filter.FailsVendorReadQualityFilter
 
FASTA_EXTENSIONS - Static variable in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
 
FastaSequenceFile - Class in htsjdk.samtools.reference

Implementation of ReferenceSequenceFile for reading from FASTA files.

FastaSequenceFile(File, boolean) - Constructor for class htsjdk.samtools.reference.FastaSequenceFile

Constructs a FastaSequenceFile that reads from the specified file.

FastaSequenceFile(Path, boolean) - Constructor for class htsjdk.samtools.reference.FastaSequenceFile

Constructs a FastaSequenceFile that reads from the specified file.

FastaSequenceIndex - Class in htsjdk.samtools.reference

Reads a fasta index file (.fai), as generated by `samtools faidx`.

FastaSequenceIndex(File) - Constructor for class htsjdk.samtools.reference.FastaSequenceIndex

Build a sequence index from the specified file.

FastaSequenceIndex(Path) - Constructor for class htsjdk.samtools.reference.FastaSequenceIndex

Build a sequence index from the specified file.

FastaSequenceIndex() - Constructor for class htsjdk.samtools.reference.FastaSequenceIndex

Empty, protected constructor for unit testing.

FastGenotype - Class in htsjdk.variant.variantcontext

This class encompasses all the basic information about a genotype.

FastGenotype(String, List<Allele>, boolean, int, int, int[], int[], String, Map<String, Object>) - Constructor for class htsjdk.variant.variantcontext.FastGenotype

The only way to make one of these, for use by GenotypeBuilder only

FastLineReader - Class in htsjdk.samtools.util

Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding,
 in order to improve performance.

FastLineReader(InputStream) - Constructor for class htsjdk.samtools.util.FastLineReader
 
FastqConstants - Class in htsjdk.samtools.fastq
 
FastqConstants() - Constructor for class htsjdk.samtools.fastq.FastqConstants
 
FastqConstants.FastqExtensions - Enum in htsjdk.samtools.fastq
 
FastqQualityFormat - Enum in htsjdk.samtools.util

Enumeration for FastQ quality score formats formats.

FastqReader - Class in htsjdk.samtools.fastq

Reads a FASTQ file with four lines per record.

FastqReader(File) - Constructor for class htsjdk.samtools.fastq.FastqReader
 
FastqReader(File, boolean) - Constructor for class htsjdk.samtools.fastq.FastqReader

Constructor

FastqReader(BufferedReader) - Constructor for class htsjdk.samtools.fastq.FastqReader
 
FastqReader(File, BufferedReader, boolean) - Constructor for class htsjdk.samtools.fastq.FastqReader

Constructor

FastqReader(File, BufferedReader) - Constructor for class htsjdk.samtools.fastq.FastqReader
 
FastqRecord - Class in htsjdk.samtools.fastq

Represents a fastq record, fairly literally, i.e.

FastqRecord(String, String, String, String) - Constructor for class htsjdk.samtools.fastq.FastqRecord
 
FastqRecord(FastqRecord) - Constructor for class htsjdk.samtools.fastq.FastqRecord

copy constructor

fastqToPhred(String) - Static method in class htsjdk.samtools.SAMUtils

Convert a string with phred scores in printable ASCII FASTQ format to an array
 of binary phred scores.

fastqToPhred(byte[]) - Static method in class htsjdk.samtools.SAMUtils

Converts printable qualities in Sanger fastq format to binary phred scores.

fastqToPhred(char) - Static method in class htsjdk.samtools.SAMUtils

Convert a single printable ASCII FASTQ format phred score to binary phred score.

FastqWriter - Interface in htsjdk.samtools.fastq

Simple interface for a class that can write out fastq records.

FastqWriterFactory - Class in htsjdk.samtools.fastq

Factory class for creating FastqWriter objects.

FastqWriterFactory() - Constructor for class htsjdk.samtools.fastq.FastqWriterFactory
 
Feature - Interface in htsjdk.tribble

Represents a locus on a reference sequence.

FeatureCodec<FEATURE_TYPE extends Feature,SOURCE> - Interface in htsjdk.tribble

The base interface for classes that read in features.

FeatureCodecHeader - Class in htsjdk.tribble

A class to represent a header of a feature containing file.

FeatureCodecHeader(Object, long) - Constructor for class htsjdk.tribble.FeatureCodecHeader

Create a FeatureCodecHeader indicating the contents of the header (can be null)
 and the byte position in the file where the header ends (not inclusive).

FeatureFileDoesntExist(String, String) - Constructor for exception htsjdk.tribble.TribbleException.FeatureFileDoesntExist
 
featurePositionCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
FeatureReader<T extends Feature> - Interface in htsjdk.tribble

the basic interface that feature sources need to match

featuresCodeCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
FIELD_SEPARATOR_CHAR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
FILE_TYPES - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
 
FileAppendStreamLRUCache - Class in htsjdk.samtools.util

LRU cache of OutputStreams to handle situation in which it is necessary to have more FileOutputStreams
 than resource limits will allow.

FileAppendStreamLRUCache(int) - Constructor for class htsjdk.samtools.util.FileAppendStreamLRUCache
 
fileExtension() - Method in class htsjdk.samtools.SamReader.Type

The recommended file extension for SAMs of this type, without a period.

fileHeaderTypeIdentifier - Variable in enum htsjdk.tribble.index.AbstractIndex.IndexType
 
fileNameSuffix - Variable in enum htsjdk.samtools.SamIndexes
 
fileOrderCompare(SAMRecord, SAMRecord) - Method in interface htsjdk.samtools.SAMRecordComparator

Less stringent compare method than the regular compare.

fileOrderCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordCoordinateComparator

Less stringent compare method than the regular compare.

fileOrderCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordDuplicateComparator

Less stringent than duplicateSetCompare, such that two records are equal enough such that their ordering in a sorted SAM file would be arbitrary.

fileOrderCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordQueryHashComparator

Compares two records based on an integer hash of their read names.

fileOrderCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordQueryNameComparator

Less stringent compare method than the regular compare.

fileSuffix(File) - Static method in class htsjdk.samtools.util.IOUtil

Returns the name of the file extension (i.e.

FileTruncatedException - Exception in htsjdk.samtools

Thrown when it is possible to detect that a SAM or BAM file is truncated.

FileTruncatedException() - Constructor for exception htsjdk.samtools.FileTruncatedException
 
FileTruncatedException(String) - Constructor for exception htsjdk.samtools.FileTruncatedException
 
FileTruncatedException(String, Throwable) - Constructor for exception htsjdk.samtools.FileTruncatedException
 
FileTruncatedException(Throwable) - Constructor for exception htsjdk.samtools.FileTruncatedException
 
filter(String) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Most efficient version of setting filters -- just set the filters string to filters

filter(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
 
FILTER_CODE_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
FILTER_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
 
filterHash - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
FilteringIterator - Class in htsjdk.samtools.filter

Deprecated.

FilteringIterator(Iterator<SAMRecord>, SamRecordFilter, boolean) - Constructor for class htsjdk.samtools.filter.FilteringIterator

Deprecated.
 
FilteringIterator(Iterator<SAMRecord>, SamRecordFilter) - Constructor for class htsjdk.samtools.filter.FilteringIterator

Deprecated.
 
FilteringIterator - Class in htsjdk.variant.variantcontext.filter

Deprecated.

FilteringIterator(Iterator<VariantContext>, VariantContextFilter) - Constructor for class htsjdk.variant.variantcontext.filter.FilteringIterator

Deprecated.
 
FilteringSamIterator - Class in htsjdk.samtools.filter

Filtering Iterator which takes a filter and an iterator and iterates through only those records
 which are not rejected by the filter.

FilteringSamIterator(Iterator<SAMRecord>, SamRecordFilter, boolean) - Constructor for class htsjdk.samtools.filter.FilteringSamIterator

Constructor

FilteringSamIterator(Iterator<SAMRecord>, SamRecordFilter) - Constructor for class htsjdk.samtools.filter.FilteringSamIterator

Constructor

FilteringVariantContextIterator - Class in htsjdk.variant.variantcontext.filter

A filtering iterator for VariantContexts that takes a base iterator and a VariantContextFilter.

FilteringVariantContextIterator(Iterator<VariantContext>, VariantContextFilter) - Constructor for class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator

Constructor of an iterator based on the provided iterator and predicate.

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.AggregateFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.AggregateFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.AlignedFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.AlignedFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.DuplicateReadFilter
 
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.DuplicateReadFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.FailsVendorReadQualityFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.FailsVendorReadQualityFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.InsertSizeFilter
 
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.InsertSizeFilter
 
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.IntervalFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.IntervalFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.IntervalKeepPairFilter

Determines whether a SAMRecord matches this filter.

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.IntervalKeepPairFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.JavascriptSamRecordFilter

return true of both records are filteredOut (AND)

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.JavascriptSamRecordFilter

read is filtered out if the javascript program returns false

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.MappingQualityFilter
 
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.MappingQualityFilter
 
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.NotPrimaryAlignmentFilter
 
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.NotPrimaryAlignmentFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.OverclippedReadFilter
 
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.OverclippedReadFilter
 
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.ReadNameFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.ReadNameFilter

Determines whether a pair of SAMRecords matches this filter

filterOut(SAMRecord) - Method in interface htsjdk.samtools.filter.SamRecordFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in interface htsjdk.samtools.filter.SamRecordFilter

Determines whether a pair of SAMRecords matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.SecondaryAlignmentFilter

Returns true if the read is marked as secondary.

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.SecondaryAlignmentFilter

Returns true if either read is marked as secondary.

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.SecondaryOrSupplementaryFilter
 
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.SecondaryOrSupplementaryFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.SolexaNoiseFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.SolexaNoiseFilter

Determines whether a pair of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.TagFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.TagFilter

Determines whether a paired of SAMRecord matches this filter

filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.WholeReadClippedFilter

Determines whether a SAMRecord matches this filter

filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.WholeReadClippedFilter

Determines whether a paired of SAMRecord matches this filter

filters(List<String>) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Tells this builder to make a Genotype object that has had filters applied,
 which may be empty (passes) or have some value indicating the reasons
 why it's been filtered.

filters(String...) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

varargs version of #filters

filters(Set<String>) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

This builder's filters are set to this value

 filters can be null -> meaning there are no filters

filters(String...) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

VariantContextBuilder.filters

filtersWereApplied() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
filtersWereApplied() - Method in class htsjdk.variant.variantcontext.VariantContext
 
finalize() - Method in class htsjdk.samtools.util.DiskBackedQueue

Clean up disk resources in case clear() has not been explicitly called (as would be preferable)
 Closes the input and output streams associated with this DiskBackedQueue and deletes the temporary file

finalizeAll() - Method in class htsjdk.samtools.util.ResourceLimitedMap

Remove all the values from the map, and call functory.finalizeValue() on each of them.

finalizeIndex() - Method in class htsjdk.tribble.index.AbstractIndex
 
finalizeIndex(long) - Method in class htsjdk.tribble.index.DynamicIndexCreator
 
finalizeIndex(long) - Method in interface htsjdk.tribble.index.IndexCreator

Create the index, given the stream of features passed in to this point

finalizeIndex(long) - Method in class htsjdk.tribble.index.interval.IntervalIndexCreator

finalize the index; create a tree index given the feature list passed in so far

finalizeIndex(long) - Method in class htsjdk.tribble.index.linear.LinearIndexCreator

finalize the index; producing an index object

finalizeIndex(long) - Method in class htsjdk.tribble.index.tabix.TabixIndexCreator
 
finalizeValue(Key, Value) - Method in interface htsjdk.samtools.util.ResourceLimitedMapFunctor

Clean up an existing value in conjunction with removing from ResourceLimitedMap.

find(List<CRAIEntry>, int, int, int) - Static method in class htsjdk.samtools.cram.CRAIIndex
 
find(short) - Method in class htsjdk.samtools.SAMBinaryTagAndValue

Returns the SAMBinaryTagAndValue that contains the required tag, or null if not contained.

find(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Find an interval.

findByIndex(int) - Method in class htsjdk.samtools.util.IntervalTree

Find the nth interval in the tree.

findByName(String) - Static method in enum htsjdk.samtools.SAMFlag
 
findIndex(File) - Static method in class htsjdk.samtools.SamFiles

Finds the index file associated with the provided SAM file.

findIndex(Path) - Static method in class htsjdk.samtools.SamFiles

Finds the index file associated with the provided SAM file.

findLastAlignedEntry(List<CRAIEntry>) - Static method in class htsjdk.samtools.cram.CRAIIndex

Find index of the last aligned entry in the list.

findOverlapping(Interval) - Method in class htsjdk.tribble.index.interval.IntervalTree
 
findQualityTrimPoint(byte[], int) - Static method in class htsjdk.samtools.util.TrimmingUtil

Implements phred-style quality trimming.

findVirtualOffsetOfFirstRecordInBam(File) - Static method in class htsjdk.samtools.SAMUtils

Returns the virtual file offset of the first record in a BAM file - i.e.

finish() - Method in class htsjdk.samtools.BAMIndexer

After all the alignment records have been processed, finish is called.

finish() - Method in class htsjdk.samtools.CRAMBAIIndexer

After all the slices have been processed, finish is called.

finish(boolean) - Method in class htsjdk.samtools.CRAMContainerStreamWriter

Finish writing to the stream.

finish() - Method in class htsjdk.samtools.CRAMCRAIIndexer

Finish creating the index by writing the accumulated entries out to the stream.

finish() - Method in class htsjdk.samtools.CRAMFileWriter
 
finish() - Method in class htsjdk.samtools.SAMFileWriterImpl

Do any required flushing here.

finish() - Method in class htsjdk.samtools.SAMTextWriter

Do any required flushing here.

FIRST_OF_PAIR_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
FIVE_GBS - Static variable in class htsjdk.samtools.util.IOUtil
 
FixBAMFile - Class in htsjdk.samtools
 
FixBAMFile() - Constructor for class htsjdk.samtools.FixBAMFile
 
Flag(VCFCompoundHeaderLine, Map<String, Integer>) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Flag
 
flags - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
flags - Variable in class htsjdk.tribble.index.AbstractIndex
 
flags - Variable in class htsjdk.tribble.index.tabix.TabixFormat

Describes interpretation of file being indexed.

flankingDeletion() - Static method in class htsjdk.samtools.cram.lossy.BaseCategory
 
Float(VCFCompoundHeaderLine, Map<String, Integer>) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Float
 
FLOW_ORDER_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
flush() - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
flush() - Method in class htsjdk.samtools.fastq.BasicFastqWriter
 
flush() - Method in class htsjdk.samtools.util.AsciiWriter

flushes underlying OutputStream

flush() - Method in class htsjdk.samtools.util.BlockCompressedOutputStream

WARNING: flush() affects the output format, because it causes the current contents of uncompressedBuffer
 to be compressed and written, even if it isn't full.

flush() - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
 
flushContainer() - Method in class htsjdk.samtools.CRAMContainerStreamWriter

Complete the current container and flush it to the output stream.

format(int) - Method in enum htsjdk.samtools.SamFlagField

Returns the string associated with this flag field.

format() - Method in class htsjdk.samtools.SAMRecord

Deprecated.
This method is not guaranteed to return a valid SAM text representation of the SAMRecord.
 To get standard SAM text representation, SAMRecord.getSAMString().


format() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
format(short) - Method in class htsjdk.samtools.util.FormatUtil

Formats a short to an integer string.

format(int) - Method in class htsjdk.samtools.util.FormatUtil

Formats an int to an integer string.

format(long) - Method in class htsjdk.samtools.util.FormatUtil

Formats a long to an integer string.

format(float) - Method in class htsjdk.samtools.util.FormatUtil

Formats a float to a floating point string.

format(double) - Method in class htsjdk.samtools.util.FormatUtil

Formats a double to a floating point string.

format(char) - Method in class htsjdk.samtools.util.FormatUtil

Formats a char as a string.

format(Enum) - Method in class htsjdk.samtools.util.FormatUtil

Formats an enum to the String representation of an enum.

format(Date) - Method in class htsjdk.samtools.util.FormatUtil

Formats a date to a date string without time.

format(Iso8601Date) - Method in class htsjdk.samtools.util.FormatUtil

Formats date & time

format(boolean) - Method in class htsjdk.samtools.util.FormatUtil

Formats a boolean value to a String.

format(Object) - Method in class htsjdk.samtools.util.FormatUtil

Attempts to determine the type of value and format it appropriately.

FORMAT_FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
FORMAT_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
 
FormatUtil - Class in htsjdk.samtools.util

Simple class used to format object values into a standard format for printing.

FormatUtil() - Constructor for class htsjdk.samtools.util.FormatUtil

Constructs a new FormatUtil and initializes various internal formatters.

formatVCFDouble(double) - Static method in class htsjdk.variant.vcf.VCFEncoder

Takes a double value and pretty prints it to a String for display

 Large doubles => gets %.2f style formatting
 Doubles < 1 / 10 but > 1/100 => get %.3f style formatting
 Double < 1/100 => %.3e formatting

frequency - Variable in class htsjdk.samtools.cram.encoding.huffman.HuffmanTree
 
fromBufferedStream(InputStream) - Static method in class htsjdk.tribble.readers.LineReaderUtil

Deprecated.

fromBufferedStream(InputStream, Object) - Static method in class htsjdk.tribble.readers.LineReaderUtil

Deprecated.

fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.BetaIntegerEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding
 
fromByteArray(byte[]) - Method in interface htsjdk.samtools.cram.encoding.Encoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.ExternalByteArrayEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.ExternalByteEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.ExternalIntegerEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.ExternalLongEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.GammaIntegerEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.GolombIntegerEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.GolombLongEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.GolombRiceIntegerEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanByteEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.NullEncoding
 
fromByteArray(byte[]) - Method in class htsjdk.samtools.cram.encoding.SubexponentialIntegerEncoding
 
fromCigarOperators(List<CigarOperator>) - Static method in class htsjdk.samtools.Cigar

build a new Cigar object from a list of cigar operators.

fromContainer(Container) - Static method in class htsjdk.samtools.cram.CRAIEntry
 
fromFile(File) - Static method in class htsjdk.samtools.util.IntervalList

Parses an interval list from a file.

fromFiles(Collection<File>) - Static method in class htsjdk.samtools.util.IntervalList

Calls IntervalList.fromFile(java.io.File) on the provided files, and returns their IntervalList.union(java.util.Collection).

fromFileSpan(SeekableStream, long[]) - Static method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
 
fromGLField(String) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

Deprecated.

fromHexDigit(char) - Static method in class htsjdk.samtools.util.StringUtil
 
fromInt(int) - Static method in enum htsjdk.samtools.cram.encoding.rans.RANS.ORDER
 
fromLog10Likelihoods(double[]) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
fromName(SAMFileHeader, String) - Static method in class htsjdk.samtools.util.IntervalList

Creates an IntervalList from the given sequence name

fromPLField(String) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
fromPLs(int[]) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
fromReader(BufferedReader) - Static method in class htsjdk.samtools.util.IntervalList

Parses an interval list from a reader in a stream based fashion.

fromStringReader(StringReader) - Static method in class htsjdk.tribble.readers.LineReaderUtil

Deprecated.

fromStringReader(StringReader, Object) - Static method in class htsjdk.tribble.readers.LineReaderUtil

Deprecated.

fromVcf(File) - Static method in class htsjdk.variant.vcf.VCFFileReader

Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists.

fromVcf(File, boolean) - Static method in class htsjdk.variant.vcf.VCFFileReader
 
fromVcf(VCFFileReader) - Static method in class htsjdk.variant.vcf.VCFFileReader

Converts a vcf to an IntervalList.

fromVcf(VCFFileReader, boolean) - Static method in class htsjdk.variant.vcf.VCFFileReader
 
FTGenotypesWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.FTGenotypesWriter
 
FTPClient - Class in htsjdk.samtools.util.ftp
 
FTPClient() - Constructor for class htsjdk.samtools.util.ftp.FTPClient
 
FTPHelper - Class in htsjdk.tribble.util
 
FTPHelper(URL) - Constructor for class htsjdk.tribble.util.FTPHelper
 
FTPReply - Class in htsjdk.samtools.util.ftp
 
FTPReply(BufferedReader) - Constructor for class htsjdk.samtools.util.ftp.FTPReply
 
FTPStream - Class in htsjdk.samtools.util.ftp

A "non-seekable" ftp stream.

FTPStream(FTPClient) - Constructor for class htsjdk.samtools.util.ftp.FTPStream
 
FTPUtils - Class in htsjdk.samtools.util.ftp
 
FTPUtils() - Constructor for class htsjdk.samtools.util.ftp.FTPUtils
 
FullBEDFeature - Class in htsjdk.tribble.bed

Object for full BED file.

FullBEDFeature(String, int, int) - Constructor for class htsjdk.tribble.bed.FullBEDFeature
 
FullBEDFeature.Exon - Class in htsjdk.tribble.bed

A sub region of a feature.

FullBEDFeature.Exon2 - Class in htsjdk.tribble.bed
 
fullyDecode(VCFHeader, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext

Return a VC equivalent to this one but where all fields are fully decoded

 See VariantContext document about fully decoded

fullyDecoded(boolean) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Sets this builder's fully decoded state to true.

FwdIterator(IntervalTree.Node<V>) - Constructor for class htsjdk.samtools.util.IntervalTree.FwdIterator
 
FZ - Variable in class htsjdk.samtools.SAMTagUtil
 




G

g - Static variable in class htsjdk.samtools.util.SequenceUtil

Byte typed variables for all normal bases.

G - Static variable in class htsjdk.samtools.util.SequenceUtil

Byte typed variables for all normal bases.

GammaIntegerEncoding - Class in htsjdk.samtools.cram.encoding
 
GammaIntegerEncoding() - Constructor for class htsjdk.samtools.cram.encoding.GammaIntegerEncoding
 
GammaIntegerEncoding(int) - Constructor for class htsjdk.samtools.cram.encoding.GammaIntegerEncoding
 
gatherWithBlockCopying(List<File>, File, boolean, boolean) - Static method in class htsjdk.samtools.BamFileIoUtils

Assumes that all inputs and outputs are block compressed VCF files and copies them without decompressing and parsing
 most of the gzip blocks.

GaveUpException(String) - Constructor for exception htsjdk.samtools.cram.ref.EnaRefService.GaveUpException
 
GeliTextCodec - Class in htsjdk.tribble.gelitext

Deprecated.
This is deprecated and unsupported.


GeliTextCodec() - Constructor for class htsjdk.tribble.gelitext.GeliTextCodec

Deprecated.
 
GeliTextFeature - Class in htsjdk.tribble.gelitext

Deprecated.
this is deprecated and no longer supported


GeliTextFeature(String, long, char, int, int, DiploidGenotype, double, double, double[]) - Constructor for class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
Create a geli text feature, given:

GeneralUtils - Class in htsjdk.variant.utils

Constants and utility methods used throughout the VCF/BCF/VariantContext classes

GeneralUtils() - Constructor for class htsjdk.variant.utils.GeneralUtils
 
generateAllKmers(int) - Static method in class htsjdk.samtools.util.SequenceUtil

Generates all possible unambiguous kmers (upper-case) of length and returns them as byte[]s.

generateBestGuess(QualityEncodingDetector.FileContext, FastqQualityFormat) - Method in class htsjdk.samtools.util.QualityEncodingDetector

Make the best guess at the quality format.

generateCandidateQualities(boolean) - Method in class htsjdk.samtools.util.QualityEncodingDetector

Processes collected quality data and applies rules to determine which quality formats are possible.

generateException(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
 
generateException(String, int) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec
 
generateIndexContent() - Method in class htsjdk.samtools.BinningIndexBuilder

Creates the BAMIndexContent for this reference.

generateLazyNowInstance() - Static method in class htsjdk.samtools.util.RelativeIso8601Date

Returns a "lazy now" instance.

GENERIC_FLAGS - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
 
GenericInts(VCFCompoundHeaderLine, Map<String, Integer>) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.GenericInts
 
GenericSiteWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenericSiteWriter
 
GenomicIndexUtil - Class in htsjdk.samtools

Constants and methods used by BAM and Tribble indices

GenomicIndexUtil() - Constructor for class htsjdk.samtools.GenomicIndexUtil
 
Genotype - Class in htsjdk.variant.variantcontext

This class encompasses all the basic information about a genotype.

Genotype(String, String) - Constructor for class htsjdk.variant.variantcontext.Genotype
 
GENOTYPE_ALLELE_DEPTHS - Static variable in class htsjdk.variant.vcf.VCFConstants
 
GENOTYPE_FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
GENOTYPE_FIELD_SEPARATOR_CHAR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
GENOTYPE_FILTER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
GENOTYPE_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
GENOTYPE_LIKELIHOODS_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants

Deprecated.

GENOTYPE_PL_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
GENOTYPE_POSTERIORS_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
GENOTYPE_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
GenotypeBuilder - Class in htsjdk.variant.variantcontext

A builder class for genotypes

 Provides convenience setter methods for all of the Genotype field
 values.

GenotypeBuilder() - Constructor for class htsjdk.variant.variantcontext.GenotypeBuilder

Create a empty builder.

GenotypeBuilder(String) - Constructor for class htsjdk.variant.variantcontext.GenotypeBuilder

Create a builder using sampleName.

GenotypeBuilder(String, List<Allele>) - Constructor for class htsjdk.variant.variantcontext.GenotypeBuilder

Make a builder using sampleName and alleles for starting values

GenotypeBuilder(Genotype) - Constructor for class htsjdk.variant.variantcontext.GenotypeBuilder

Create a new builder starting with the values in Genotype g

genotypeCounts - Variable in class htsjdk.variant.variantcontext.VariantContext

Counts for each of the possible Genotype types in this context

GenotypeJEXLContext - Class in htsjdk.variant.variantcontext
 
GenotypeJEXLContext(VariantContext, Genotype) - Constructor for class htsjdk.variant.variantcontext.GenotypeJEXLContext
 
GenotypeLikelihoods - Class in htsjdk.variant.variantcontext
 
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair - Class in htsjdk.variant.variantcontext
 
GenotypeLikelihoodsAllelePair(int, int) - Constructor for class htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
 
genotypeNames(Collection<Genotype>) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
 
genotypeParts - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
GenotypeQualityFilter - Class in htsjdk.variant.variantcontext.filter

A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).

GenotypeQualityFilter(int, String) - Constructor for class htsjdk.variant.variantcontext.filter.GenotypeQualityFilter

Constructor for a filter that will keep VC for which the
 genotype quality (GQ) of sample passes a threshold.

GenotypeQualityFilter(int) - Constructor for class htsjdk.variant.variantcontext.filter.GenotypeQualityFilter

Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.

genotypes - Variable in class htsjdk.variant.variantcontext.VariantContext

A mapping from sampleName -> genotype objects for all genotypes associated with this context

genotypes(GenotypesContext) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells this builder that the resulting VariantContext should use this genotype's GenotypeContext.

genotypes(Collection<Genotype>) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells this builder that the resulting VariantContext should use a GenotypeContext containing genotypes

 Note that genotypes can be null, meaning there are no genotypes

genotypes(Genotype...) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells this builder that the resulting VariantContext should use a GenotypeContext containing genotypes

GenotypesContext - Class in htsjdk.variant.variantcontext

Represents an ordered collection of Genotype objects

GenotypesContext() - Constructor for class htsjdk.variant.variantcontext.GenotypesContext

Create an empty GenotypeContext

GenotypesContext(int) - Constructor for class htsjdk.variant.variantcontext.GenotypesContext

Create an empty GenotypeContext, with initial capacity for n elements

GenotypesContext(ArrayList<Genotype>) - Constructor for class htsjdk.variant.variantcontext.GenotypesContext

Create an GenotypeContext containing genotypes

GenotypesContext(ArrayList<Genotype>, Map<String, Integer>, List<String>) - Constructor for class htsjdk.variant.variantcontext.GenotypesContext

Create a fully resolved GenotypeContext containing genotypes, sample lookup table,
 and sorted sample names

genotypesNoValidation(GenotypesContext) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
 
GenotypesWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
 
GenotypeType - Enum in htsjdk.variant.variantcontext

Summary types for Genotype objects

get(int) - Method in class htsjdk.samtools.cram.common.IntHashMap


 Returns the value to which the specified key is mapped in this map.

get(int) - Method in class htsjdk.samtools.LinearIndex
 
get(int, String, int) - Method in class htsjdk.samtools.reference.ReferenceSequenceFileWalker

Ensure that the requested sequence is loaded.

get(int) - Method in class htsjdk.samtools.reference.ReferenceSequenceFileWalker

Get reference sequence without validating name or length.

get(int) - Method in class htsjdk.samtools.sra.ReferenceCache

This method returns Reference objects by reference indexes in SAM header
 Those objects do not maintain thread safety

get(Object) - Method in class htsjdk.samtools.util.CollectionUtil.DefaultingMap
 
get(K) - Method in class htsjdk.samtools.util.Histogram

Retrieves the bin associated with the given key.

get(int, int) - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask

It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

get(Object) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
get(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
get() - Method in class htsjdk.samtools.util.Lazy

Returns the instance associated with this Lazy, initializing it if necessary.

get(int, int) - Method in interface htsjdk.samtools.util.ReferenceSequenceMask

It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

get(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap

Return an existing value, or create a new one if necessary.

get(int, int) - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
 
get(String) - Method in class htsjdk.variant.variantcontext.GenotypeJEXLContext
 
get(int) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
get(String) - Method in class htsjdk.variant.variantcontext.GenotypesContext

Gets sample associated with this sampleName, or null if none is found

getAcceptedCount() - Method in class htsjdk.samtools.DownsamplingIterator

Returns the number of records returned since creation of the last call to resetStatistics.

getAcceptedFraction() - Method in class htsjdk.samtools.DownsamplingIterator

Gets the fraction of records accepted since creation or the last call to resetStatistics().

getAccessor(String) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors

Return an accessor for field, or null if none exists

getAD() - Method in class htsjdk.variant.variantcontext.FastGenotype
 
getAD() - Method in class htsjdk.variant.variantcontext.Genotype
 
getAlignedRecordCount() - Method in class htsjdk.samtools.BAMIndexMetaData
 
getAlignmentBlocks() - Method in class htsjdk.samtools.SAMRecord

Returns blocks of the read sequence that have been aligned directly to the
 reference sequence.

getAlignmentBlocks(Cigar, int, String) - Static method in class htsjdk.samtools.SAMUtils

Given a Cigar, Returns blocks of the sequence that have been aligned directly to the
 reference sequence.

getAlignmentEnd() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
getAlignmentEnd() - Method in class htsjdk.samtools.SAMRecord
 
getAlignmentSpan() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
getAlignmentStart() - Method in class htsjdk.samtools.SAMRecord
 
getAlignmentStart() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getAll() - Method in class htsjdk.samtools.util.OverlapDetector

Gets all the objects that could be returned by the overlap detector.

getAllChunks() - Method in class htsjdk.samtools.BinningIndexContent
 
getAllele(int) - Method in class htsjdk.variant.variantcontext.FastGenotype
 
getAllele(int) - Method in class htsjdk.variant.variantcontext.Genotype

Get the ith allele in this genotype

getAllele(String) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAllele(byte[]) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAlleleIndex(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext

Lookup the index of allele in this variant context

getAlleleIndices(Collection<Allele>) - Method in class htsjdk.variant.variantcontext.VariantContext

Return the allele index #getAlleleIndex for each allele in alleles

getAllelePair(int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

Get the diploid allele index pair for the given PL index

getAllelePairUsingDeprecatedOrdering(int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

Deprecated.

getAlleles() - Method in class htsjdk.variant.variantcontext.FastGenotype
 
getAlleles() - Method in class htsjdk.variant.variantcontext.Genotype
 
getAlleles(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

Get the allele ploidy indices for the given PL index
 Must use the same ploidy as @see #initializeAnyploidPLIndexToAlleleIndices

getAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext

Gets the alleles.

getAlleles() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
 
getAlleleStrings() - Method in class htsjdk.variant.variantcontext.Genotype

Utility that returns a list of allele strings corresponding to the alleles in this sample

getAllHistograms() - Method in class htsjdk.samtools.metrics.MetricsFile
 
getAltAlleleWithHighestAlleleCount() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAlternateAllele(int) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAlternateAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext

Gets the alternate alleles.

getAminoAcidNumber(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
 
getAnyAttribute(String) - Method in class htsjdk.variant.variantcontext.Genotype

A totally generic getter, that allows you to get specific keys that correspond
 to even inline values (GQ, for example).

getAsMap(boolean) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
getAsPLs() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
getAssembly() - Method in class htsjdk.samtools.SAMSequenceRecord
 
getAsString() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
getAsTags() - Method in class htsjdk.samtools.cram.digest.ContentDigests
 
getAsVector() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

The genotypes likelihoods in -10log10(x) vector format.

getAttribute(String) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
 
getAttribute(short) - Method in class htsjdk.samtools.BAMRecord
 
getAttribute(short) - Method in class htsjdk.samtools.cram.structure.Slice

Get tag value attached to the slice.

getAttribute(String) - Method in class htsjdk.samtools.SAMRecord

Get the value for a SAM tag.

getAttribute(short) - Method in class htsjdk.samtools.SAMRecord
 
getAttribute(short) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getAttribute(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttribute(String, Object) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttribute(String) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttribute(String, Object) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributeAsBoolean(String, boolean) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttributeAsBoolean(String, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributeAsDouble(String, double) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttributeAsDouble(String, double) - Method in class htsjdk.variant.variantcontext.Genotype

Deprecated.

getAttributeAsDouble(String, double) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributeAsDoubleList(String, Double) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttributeAsDoubleList(String, double) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributeAsInt(String, int) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttributeAsInt(String, int) - Method in class htsjdk.variant.variantcontext.Genotype

Deprecated.

getAttributeAsInt(String, int) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributeAsIntList(String, Integer) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttributeAsIntList(String, int) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributeAsList(String) - Method in class htsjdk.variant.variantcontext.CommonInfo

Gets the attributes from a key as a list.

getAttributeAsList(String) - Method in class htsjdk.variant.variantcontext.VariantContext

returns the value as an empty list if the key was not found,
        as a java.util.List if the value is a List or an Array,
        as a Collections.singletonList if there is only one value

getAttributeAsString(String, String) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttributeAsString(String, String) - Method in class htsjdk.variant.variantcontext.Genotype

Deprecated.

getAttributeAsString(String, String) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributeAsStringList(String, String) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttributeAsStringList(String, String) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributes() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord

Returns the Set of attributes.

getAttributes() - Method in class htsjdk.samtools.SAMRecord
 
getAttributes() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getAttributes() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getAttributesBinarySize() - Method in class htsjdk.samtools.BAMRecord

Depending on the concrete implementation, the binary file size of attributes may be known without
 computing them all.

getAttributesBinarySize() - Method in class htsjdk.samtools.SAMRecord

Depending on the concrete implementation, the binary file size of attributes may be known without
 computing them all.

getAverageFeatureSize() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
getBAMFlags(int, byte) - Static method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
getBase() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
getBase() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
getBase() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
getBase() - Method in enum htsjdk.samtools.SQTagUtil.SQBase
 
getBaseCount() - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
getBaseCount() - Method in class htsjdk.samtools.util.IntervalList

Gets the (potentially redundant) sum of the length of the intervals in the list.

getBaseQualities() - Method in class htsjdk.samtools.BAMRecord
 
getBaseQualities() - Method in class htsjdk.samtools.SAMRecord

Do not modify the value returned by this method.

getBaseQualities() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getBaseQualities() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
getBaseQuality() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
getBaseQuality(int) - Method in class htsjdk.samtools.util.EdgingRecordAndOffset
 
getBaseQualityHeader() - Method in class htsjdk.samtools.fastq.FastqRecord
 
getBaseQualityString() - Method in class htsjdk.samtools.fastq.FastqRecord
 
getBaseQualityString() - Method in class htsjdk.samtools.SAMRecord
 
getBases() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
 
getBases() - Method in class htsjdk.samtools.reference.ReferenceSequence

Gets the array of bases that define this sequence.

getBases() - Method in class htsjdk.variant.variantcontext.Allele

Return the DNA bases segregating in this allele.

getBaseString() - Method in class htsjdk.samtools.reference.ReferenceSequence

Returns the bases represented by this ReferenceSequence as a String.

getBaseString() - Method in class htsjdk.variant.variantcontext.Allele

Return the DNA bases segregating in this allele in String format.

getBinaryAttributes() - Method in class htsjdk.samtools.BAMRecord
 
getBinaryAttributes() - Method in class htsjdk.samtools.SAMRecord
 
getBinaryAttributes() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getBinLabel() - Method in class htsjdk.samtools.util.Histogram
 
getBinNumber() - Method in class htsjdk.samtools.Bin
 
getBins() - Method in class htsjdk.samtools.BinList

Retrieves the bins stored in this list.

getBins() - Method in class htsjdk.samtools.BinningIndexContent
 
getBinSize() - Method in class htsjdk.tribble.index.linear.LinearIndexCreator
 
getBinsOverlapping(int, int, int) - Method in interface htsjdk.samtools.BrowseableBAMIndex

Get a list of bins in the BAM file that may contain SAMRecords for the given range.

getBinsOverlapping(int, int, int) - Method in class htsjdk.samtools.SRAIndex

Provides a list of bins that contain bases at requested positions

getBlock() - Method in class htsjdk.tribble.index.interval.Interval
 
getBlockAddress(long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
 
getBlockOffset(long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
 
getBlocks(String, int, int) - Method in class htsjdk.tribble.index.AbstractIndex
 
getBlocks(String) - Method in class htsjdk.tribble.index.AbstractIndex
 
getBlocks() - Method in interface htsjdk.tribble.index.ChrIndex
 
getBlocks(int, int) - Method in interface htsjdk.tribble.index.ChrIndex
 
getBlocks(String, int, int) - Method in interface htsjdk.tribble.index.Index

Query the index.

getBlocks() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
 
getBlocks(int, int) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
 
getBlocks() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
getBlocks(int, int) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
getBlocks(String, int, int) - Method in class htsjdk.tribble.index.tabix.TabixIndex
 
getBlockSize() - Method in class htsjdk.variant.bcf2.BCF2Decoder

The size of the current block in bytes

getBlockStats(boolean) - Method in class htsjdk.tribble.index.AbstractIndex
 
getBrowseableIndex() - Method in class htsjdk.samtools.CRAMFileReader
 
getBrowseableIndex() - Method in interface htsjdk.samtools.SamReader.Indexing

Gets an index tagged with the BrowseableBAMIndex interface.

getBrowseableIndex() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
getBrowseableIndex() - Method in class htsjdk.samtools.SRAFileReader

Gets an index tagged with the BrowseableBAMIndex interface.

getBuffer() - Method in class htsjdk.samtools.cram.io.ExposedByteArrayOutputStream
 
getBufferedStream(SeekableStream) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory

Return a buffered SeekableStream which wraps the input stream
 using the default buffer size

getBufferedStream(SeekableStream, int) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory

Return a buffered SeekableStream which wraps the input stream

getByte() - Method in class htsjdk.samtools.util.FastLineReader
 
getByteArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord

Will work for signed byte array, unsigned byte array, or old-style hex array

getByteAttribute(String) - Method in class htsjdk.samtools.SAMRecord

Get the tag value and attempt to coerce it into the requested type.

getByteSize(Version, Container) - Static method in class htsjdk.samtools.cram.structure.ContainerIO

Calculates the byte size of a container based on the CRAM version.

getCachedString(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec

Return a cached copy of the supplied string.

getCalledChrCount() - Method in class htsjdk.variant.variantcontext.VariantContext

Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS)

getCalledChrCount(Set<String>) - Method in class htsjdk.variant.variantcontext.VariantContext

Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS)

getCalledChrCount(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext

Returns the number of chromosomes carrying allele A in the genotypes

getCalledChrCount(Allele, Set<String>) - Method in class htsjdk.variant.variantcontext.VariantContext

Returns the number of chromosomes carrying allele A in the genotypes

getCanonicalRecordName(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Returns a string that is the the read group ID and read name separated by a colon.

getCaptureTags() - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
getCaptureTags() - Method in class htsjdk.samtools.CRAMFileWriter
 
getCdEnd() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon

Method description

getCdEnd() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Method description

getCdStart() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon

Method description

getCdStart() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Method description

getCharacterAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getChr() - Method in interface htsjdk.tribble.Feature

Deprecated.
use getContig() instead


getChrIndexClass() - Method in class htsjdk.tribble.index.AbstractIndex

returns the class for the index type

getChrIndexClass() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
 
getChrIndexClass() - Method in class htsjdk.tribble.index.linear.LinearIndex
 
getChromosomes() - Method in class htsjdk.tribble.readers.TabixReader

return the chromosomes in that tabix file

getChunk() - Method in interface htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
 
getChunkEnd() - Method in class htsjdk.samtools.Chunk
 
getChunkList() - Method in class htsjdk.samtools.Bin

Gets the list of chunks associated with this bin.

getChunks() - Method in class htsjdk.samtools.BAMFileSpan

Gets the constituent chunks stored in this span.

getChunksOverlapping(int, int) - Method in class htsjdk.samtools.BinningIndexContent
 
getChunkStart() - Method in class htsjdk.samtools.Chunk
 
getCigar() - Method in class htsjdk.samtools.BAMRecord
 
getCigar() - Method in class htsjdk.samtools.SAMRecord

Do not modify the value returned by this method.

getCigar() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getCigarElement(int) - Method in class htsjdk.samtools.Cigar
 
getCigarElements() - Method in class htsjdk.samtools.Cigar
 
getCigarLength() - Method in class htsjdk.samtools.BAMRecord

Avoids decoding CIGAR in order to get length.

getCigarLength() - Method in class htsjdk.samtools.SAMRecord

This method is preferred over getCigar().getNumElements(), because for BAMRecord it may be faster.

getCigarString() - Method in class htsjdk.samtools.SAMRecord
 
getCigarString() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
getCode() - Method in class htsjdk.samtools.util.ftp.FTPReply

Gets server reply code from the control port after an ftp command has
 been executed.

getCodingLength() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon

Method description

getCodingLength() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Method description

getColor() - Method in interface htsjdk.tribble.bed.BEDFeature
 
getColor() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getColumnCount() - Method in class htsjdk.variant.vcf.VCFHeader
 
getCommandLine() - Method in class htsjdk.samtools.SAMProgramRecord
 
getComments() - Method in class htsjdk.samtools.SAMFileHeader
 
getCommonInfo() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getComparator() - Method in enum htsjdk.samtools.SAMFileHeader.SortOrder
 
getComparatorInstance() - Method in enum htsjdk.samtools.SAMFileHeader.SortOrder
 
getCompressedContentSize() - Method in class htsjdk.samtools.cram.structure.Block
 
getCompressionFlags() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
getCompressionLevel() - Method in class htsjdk.samtools.SAMFileWriterFactory
 
getCompressionLevel() - Static method in class htsjdk.samtools.util.IOUtil
 
getContained(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
getContentId() - Method in class htsjdk.samtools.cram.structure.Block
 
getContentLength(URL) - Static method in class htsjdk.samtools.util.ftp.FTPUtils
 
getContentLength() - Method in class htsjdk.tribble.util.FTPHelper
 
getContentLength() - Method in class htsjdk.tribble.util.HTTPHelper
 
getContentLength() - Method in class htsjdk.tribble.util.RemoteURLHelper
 
getContentLength() - Method in interface htsjdk.tribble.util.URLHelper
 
getContentsFollowing() - Method in class htsjdk.samtools.BAMFileSpan

Gets a file span over the data immediately following this span.

getContentsFollowing() - Method in interface htsjdk.samtools.SAMFileSpan

Gets a pointer over the data immediately following this span.

getContentType() - Method in class htsjdk.samtools.cram.structure.Block
 
getContig() - Method in class htsjdk.samtools.SAMRecord
 
getContig() - Method in class htsjdk.samtools.util.Interval
 
getContig() - Method in interface htsjdk.samtools.util.Locatable

Gets the contig name for the contig this is mapped to.

getContig() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getContig() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
getContig() - Method in class htsjdk.tribble.SimpleFeature
 
getContig() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getContigIndex() - Method in class htsjdk.samtools.reference.ReferenceSequence

Gets the 0-based index of this contig in the source file from which it came.

getContigIndex() - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
 
getContigLines() - Method in class htsjdk.variant.vcf.VCFHeader
 
getContigMap() - Method in class htsjdk.samtools.liftover.LiftOver
 
getCount() - Method in class htsjdk.samtools.cram.io.CountingInputStream
 
getCount() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
 
getCount() - Method in class htsjdk.samtools.util.AbstractProgressLogger

Returns the count of records processed.

getCount() - Method in class htsjdk.samtools.util.Histogram
 
getCount() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
getCount(VariantContext) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine

Get the number of values expected for this header field, given the properties of VariantContext vc

 If the count is a fixed count, return that.

getCountType() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
getCountType() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
getCRAIEntries() - Method in class htsjdk.samtools.cram.CRAIIndex
 
getCramHeader() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
 
getCramHeader() - Method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
 
getCramHeader() - Method in class htsjdk.samtools.CRAMIterator
 
getCRC32() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
 
getCrc32_BigEndian() - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
 
getCrc32_LittleEndian() - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
 
getCreator() - Method in class htsjdk.samtools.SAMFileHeader
 
getCumulativeProbability(double) - Method in class htsjdk.samtools.util.Histogram

Returns the cumulative probability of observing a value <= v when sampling the
 distribution represented by this histogram.

getCurrent() - Method in class htsjdk.samtools.NotPrimarySkippingIterator
 
getCurrent() - Method in class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
 
getCurrentInterval() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
getCycle(boolean, int, int) - Static method in class htsjdk.samtools.util.CoordMath

Determines the read cycle number for the base

getDataStream() - Method in class htsjdk.samtools.util.ftp.FTPClient
 
getDate() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

getDay() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

getDecoder(String) - Method in class htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders

Return decoder appropriate for field, or the generic decoder if no
 specialized one is bound

getDefaultBinSize() - Method in enum htsjdk.tribble.index.IndexFactory.IndexType
 
getDefaultCompressionLevel() - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream
 
getDefaultCRAMReferenceSource() - Static method in class htsjdk.samtools.cram.ref.ReferenceSource

Attempts to construct a default CRAMReferenceSource for use with CRAM files when
 one has not been explicitly provided.

getDefaultDeflaterFactory() - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream
 
getDefaultMaxRecordsInRam() - Static method in class htsjdk.samtools.SAMFileWriterImpl

When writing records that are not presorted, this number determines the 
 number of records stored in RAM before spilling to disk.

getDefaultTmpDir() - Static method in class htsjdk.samtools.util.IOUtil

Returns a default tmp directory.

getDeletedInRecord() - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
 
getDepthOfCoverage() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
getDescription() - Method in enum htsjdk.samtools.DownsamplingIteratorFactory.Strategy

Gets the description of the strategy.

getDescription() - Method in enum htsjdk.samtools.SAMFlag
 
getDescription() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getDescription() - Method in interface htsjdk.tribble.bed.BEDFeature
 
getDescription() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getDescription() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
getDescription() - Method in class htsjdk.variant.vcf.VCFFilterHeaderLine

get the "Description" field

getDictionaryString(int) - Method in class htsjdk.variant.bcf2.BCF2Codec
 
getDiscardedCount() - Method in class htsjdk.samtools.DownsamplingIterator

Returns the number of records discarded since creation of the last call to resetStatistics.

getDiscardedFraction() - Method in class htsjdk.samtools.DownsamplingIterator

Gets the fraction of records discarded since creation or the last call to resetStatistics().

getDisplayBases() - Method in class htsjdk.variant.variantcontext.Allele

Same as #getDisplayString() but returns the result as byte[].

getDisplayString() - Method in class htsjdk.variant.variantcontext.Allele

Return the printed representation of this allele.

getDownloadTriesBeforeFailing() - Method in class htsjdk.samtools.cram.ref.ReferenceSource
 
getDP() - Method in class htsjdk.variant.variantcontext.FastGenotype
 
getDP() - Method in class htsjdk.variant.variantcontext.Genotype
 
getDuplicateReadFlag() - Method in class htsjdk.samtools.SAMRecord

the read is either a PCR duplicate or an optical duplicate.

getDynamicType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.AtomicInt
 
getDynamicType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.GenericInts
 
getDynamicType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
getDynamicType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
 
getElapsedSeconds() - Method in class htsjdk.samtools.util.AbstractProgressLogger

Returns the number of seconds since progress tracking began.

getElapsedTime() - Method in class htsjdk.samtools.util.StopWatch

Returns the cumulative time between all the start() and stop() calls made to this object.

getElapsedTimeSecs() - Method in class htsjdk.samtools.util.StopWatch
 
getEncodedMatrix() - Method in class htsjdk.samtools.cram.structure.SubstitutionMatrix
 
getEnd() - Method in interface htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
 
getEnd() - Method in class htsjdk.samtools.SAMRecord

an alias of SAMRecord.getAlignmentEnd()

getEnd(int, int) - Static method in class htsjdk.samtools.util.CoordMath
 
getEnd() - Method in class htsjdk.samtools.util.Interval
 
getEnd() - Method in class htsjdk.samtools.util.IntervalTree.Node
 
getEnd() - Method in interface htsjdk.samtools.util.Locatable
 
getEnd() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getEnd() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
Return the end position following 1-based fully closed conventions.

getEnd() - Method in class htsjdk.tribble.SimpleFeature
 
getEnd() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getEndPosition() - Method in class htsjdk.tribble.index.Block
 
getErrorProbabilityFromPhredScore(int) - Static method in class htsjdk.samtools.util.QualityUtil

Given a phred score between 0 and 100 returns the probability of error.

getETag(URL) - Static method in class htsjdk.samtools.util.HttpUtils
 
getExons() - Method in interface htsjdk.tribble.bed.BEDFeature
 
getExons() - Method in class htsjdk.tribble.bed.FullBEDFeature
 
getExons() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getExtendedAttribute(String, Object) - Method in class htsjdk.variant.variantcontext.Genotype

Get the extended attribute value associated with key, if possible

getExtendedAttribute(String) - Method in class htsjdk.variant.variantcontext.Genotype

Same as #getExtendedAttribute with a null default

getExtendedAttributes() - Method in class htsjdk.variant.variantcontext.FastGenotype
 
getExtendedAttributes() - Method in class htsjdk.variant.variantcontext.Genotype

Returns the extended attributes for this object

getExtension() - Method in enum htsjdk.samtools.fastq.FastqConstants.FastqExtensions
 
getFeatureCodec(File) - Static method in class htsjdk.tribble.example.CountRecords

Return a FeatureCodec instance appropriate for the given
 featureFile.

getFeatureCount() - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
getFeatureReader(String, FeatureCodec<FEATURE, SOURCE>) - Static method in class htsjdk.tribble.AbstractFeatureReader

Calls AbstractFeatureReader.getFeatureReader(String, FeatureCodec, boolean) with requireIndex = true

getFeatureReader(String, FeatureCodec<FEATURE, SOURCE>, boolean) - Static method in class htsjdk.tribble.AbstractFeatureReader

AbstractFeatureReader.getFeatureReader(String, String, FeatureCodec, boolean) with null for indexResource

getFeatureReader(String, String, FeatureCodec<FEATURE, SOURCE>, boolean) - Static method in class htsjdk.tribble.AbstractFeatureReader
 
getFeatureReader(String, FeatureCodec<FEATURE, SOURCE>, Index) - Static method in class htsjdk.tribble.AbstractFeatureReader

Return a reader with a supplied index.

getFeaturesPerBlock() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
getFeaturesPerInterval() - Method in class htsjdk.tribble.index.interval.IntervalIndexCreator
 
getFeatureType() - Method in class htsjdk.tribble.AbstractFeatureCodec
 
getFeatureType() - Method in class htsjdk.tribble.example.ExampleBinaryCodec
 
getFeatureType() - Method in interface htsjdk.tribble.FeatureCodec


 This function returns the object the codec generates.

getFeatureType() - Method in class htsjdk.variant.bcf2.BCF2Codec
 
getField() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
getField() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
 
getFieldEncoder() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
 
getFile() - Method in class htsjdk.samtools.fastq.FastqReader
 
getFileBlock(long) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
 
getFileHeader() - Method in class htsjdk.samtools.CRAMFileReader
 
getFileHeader() - Method in interface htsjdk.samtools.SAMFileWriter
 
getFileHeader() - Method in class htsjdk.samtools.SAMFileWriterImpl
 
getFileHeader() - Method in class htsjdk.samtools.SAMLineParser

Get the File header.

getFileHeader() - Method in interface htsjdk.samtools.SamReader
 
getFileHeader() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
getFileHeader() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
getFileHeader(File) - Method in class htsjdk.samtools.SamReaderFactory

Utility method to open the file get the header and close the file

getFileHeader() - Method in class htsjdk.samtools.SRAFileReader
 
getFileHeader() - Method in class htsjdk.variant.vcf.VCFFileReader

Returns the VCFHeader associated with this VCF/BCF file.

getFilename() - Method in class htsjdk.samtools.CRAMFileWriter
 
getFilename() - Method in class htsjdk.samtools.SAMFileWriterImpl

For producing error messages.

getFilename() - Method in class htsjdk.samtools.SAMTextWriter

For producing error messages.

getFilePointer() - Method in class htsjdk.samtools.SAMFileSource

A pointer to the region on disk from which the read originated.

getFilePointer() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
 
getFilePointer() - Method in class htsjdk.samtools.util.BlockCompressedOutputStream

Encode virtual file pointer
 Upper 48 bits is the byte offset into the compressed stream of a block.

getFilePointerSpanningReads() - Method in class htsjdk.samtools.CRAMFileReader
 
getFilePointerSpanningReads() - Method in interface htsjdk.samtools.SamReader.Indexing

Gets a pointer spanning all reads in the BAM file.

getFilePointerSpanningReads() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
getFilePointerSpanningReads() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
getFilePointerSpanningReads() - Method in class htsjdk.samtools.SRAFileReader
 
getFilesMatchingRegexp(File, String) - Static method in class htsjdk.samtools.util.IOUtil
 
getFilesMatchingRegexp(File, Pattern) - Static method in class htsjdk.samtools.util.IOUtil
 
getFileSource() - Method in class htsjdk.samtools.CRAMIterator
 
getFileSource() - Method in class htsjdk.samtools.SAMRecord

Gets the source of this SAM record -- both the reader that retrieved the record and the position on disk from
 whence it came.

getFilterHeaderLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
 
getFilterLines() - Method in class htsjdk.variant.vcf.VCFHeader
 
getFilters() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getFilters() - Method in class htsjdk.variant.variantcontext.Genotype

Returns the filter string associated with this Genotype.

getFilters() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getFiltersMaybeNull() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getFiltersMaybeNull() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getFirstBinInLevel(int) - Static method in class htsjdk.samtools.AbstractBAMFileIndex

Gets the first bin in the given level.

getFirstCigarElement() - Method in class htsjdk.samtools.Cigar

returns the first cigar element

getFirstContainerOffset() - Method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
 
getFirstLocusInBin(Bin) - Method in class htsjdk.samtools.AbstractBAMFileIndex

Gets the first locus that this bin can index into.

getFirstLocusInBin(Bin) - Method in interface htsjdk.samtools.BrowseableBAMIndex

Gets the first locus that this bin can index into.

getFirstLocusInBin(Bin) - Method in class htsjdk.samtools.SRAIndex

Gets the first locus that this bin can index into.

getFirstOffset() - Method in class htsjdk.samtools.BAMFileSpan

Find the first offset in the chunk list

getFirstOfPairFlag() - Method in class htsjdk.samtools.SAMRecord

the read is the first read in a pair.

getFirstOfPairFlag() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getFlags(int) - Static method in enum htsjdk.samtools.SAMFlag
 
getFlags() - Method in class htsjdk.samtools.SAMRecord

It is preferable to use the get*Flag() methods that handle the flag word symbolically.

getFlags() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getFlags() - Method in class htsjdk.tribble.index.AbstractIndex
 
getFloatArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getFloatAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getFlowOrder() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getFormatHeaderLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
 
getFormatHeaderLines() - Method in class htsjdk.variant.vcf.VCFHeader

Returns the FORMAT HeaderLines in their original ordering

getFormatLine(String, boolean) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines

Returns the standard format line for ID.

getFormatLine(String) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines

Returns the standard format line for ID.

getFormatSpec() - Method in class htsjdk.tribble.index.tabix.TabixIndex
 
getFormatString() - Method in enum htsjdk.variant.vcf.VCFHeaderVersion
 
getFullCanonicalPath(File) - Static method in class htsjdk.samtools.util.IOUtil

Returns the full path to the file with all symbolic links resolved

getGenotype() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
getGenotype(String) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getGenotype(int) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getGenotypeFieldDecoder(String) - Method in class htsjdk.variant.bcf2.BCF2Codec
 
getGenotypeFieldWriter(String) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager

Get a genotypes writer specialized to encode values for genotypes field

getGenotypes() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
getGenotypes() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext

Overrides the genotypes accessor.

getGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getGenotypes(String) - Method in class htsjdk.variant.variantcontext.VariantContext

Returns a map from sampleName -> Genotype for the genotype associated with sampleName.

getGenotypes(Collection<String>) - Method in class htsjdk.variant.variantcontext.VariantContext

Returns a map from sampleName -> Genotype for each sampleName in sampleNames.

getGenotypes(Set<String>) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getGenotypeSamples() - Method in class htsjdk.variant.vcf.VCFHeader

get the genotyping sample names

getGenotypesOrderedBy(Iterable<String>) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getGenotypesOrderedByName() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getGenotypeString() - Method in class htsjdk.variant.variantcontext.Genotype

Return a VCF-like string representation for the alleles of this genotype.

getGenotypeString(boolean) - Method in class htsjdk.variant.variantcontext.Genotype

Return a VCF-like string representation for the alleles of this genotype.

getGeometricMean() - Method in class htsjdk.samtools.util.Histogram

Gets the geometric mean of the distribution.

getGLIndecesOfAlternateAllele(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
 
getGQ() - Method in class htsjdk.variant.variantcontext.FastGenotype
 
getGQ() - Method in class htsjdk.variant.variantcontext.Genotype

Returns a phred-scaled quality score, or -1 if none is available

getGQLog10FromLikelihoods(int, double[]) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
getGroupOrder() - Method in class htsjdk.samtools.SAMFileHeader
 
getHeader() - Method in class htsjdk.samtools.SAMRecord
 
getHeader() - Method in class htsjdk.samtools.SAMRecordSetBuilder
 
getHeader() - Method in class htsjdk.samtools.util.IntervalList

Gets the header (if there is one) for the interval list.

getHeader() - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask
 
getHeader() - Method in class htsjdk.tribble.AbstractFeatureReader

get the header

getHeader() - Method in interface htsjdk.tribble.FeatureReader
 
getHeader() - Method in class htsjdk.variant.bcf2.BCF2Codec
 
getHeader() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
 
getHeaderEnd() - Method in class htsjdk.tribble.FeatureCodecHeader
 
getHeaderField(URL, String) - Static method in class htsjdk.samtools.util.HttpUtils
 
getHeaderFields() - Method in class htsjdk.variant.vcf.VCFHeader

get the header fields in order they're presented in the input file (which is now required to be
 the order presented in the spec).

getHeaderKey() - Method in class htsjdk.samtools.filter.AbstractJavascriptFilter

returns key used for header binding

getHeaders() - Method in class htsjdk.samtools.metrics.MetricsFile

Returns the list of headers.

getHeaders(Class<? extends Header>) - Method in class htsjdk.samtools.metrics.MetricsFile

Returns the list of headers with the specified type.

getHeaders() - Method in class htsjdk.samtools.SamFileHeaderMerger

Returns the collection of readers that this header merger is working with.

getHeaderValue() - Method in class htsjdk.tribble.FeatureCodecHeader
 
getHeaderVersion(String) - Static method in enum htsjdk.variant.vcf.VCFHeaderVersion
 
getHetCount() - Method in class htsjdk.variant.variantcontext.VariantContext

Genotype-specific functions -- how many het calls are there in the genotypes?

getHistogram() - Method in class htsjdk.samtools.metrics.MetricsFile

Returns the histogram contained in the metrics file if any.

getHistogramString() - Method in enum htsjdk.samtools.SAMValidationError.Type
 
getHomRefCount() - Method in class htsjdk.variant.variantcontext.VariantContext

Genotype-specific functions -- how many hom ref calls are there in the genotypes?

getHomVarCount() - Method in class htsjdk.variant.variantcontext.VariantContext

Genotype-specific functions -- how many hom var calls are there in the genotypes?

getHours() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

getId() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord

Returns the ID tag (or equivalent) for this header record.

getId() - Method in class htsjdk.samtools.cram.structure.CramHeader
 
getId() - Method in class htsjdk.samtools.SAMProgramRecord
 
getId() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getId() - Method in class htsjdk.samtools.util.Histogram.Bin

Gets the ID of this bin.

getID() - Method in enum htsjdk.variant.bcf2.BCF2Type

The ID according to the BCF2 specification

getID() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getID() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
getID() - Method in interface htsjdk.variant.vcf.VCFIDHeaderLine
 
getID() - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
 
getIDHeaderLines() - Method in class htsjdk.variant.vcf.VCFHeader
 
getIdValue() - Method in class htsjdk.samtools.util.Histogram.Bin
 
getIgnoreTags() - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
getIgnoreTags() - Method in class htsjdk.samtools.CRAMFileWriter
 
getIndelLengths() - Method in class htsjdk.variant.variantcontext.VariantContext

Gets the sizes of the alternate alleles if they are insertion/deletion events, and returns a list of their sizes

getIndex() - Method in class htsjdk.samtools.cram.structure.ReadTag
 
getIndex() - Method in class htsjdk.samtools.CRAMFileReader
 
getIndex() - Method in interface htsjdk.samtools.SamReader.Indexing

Retrieves the index for the given file type.

getIndex() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
getIndex() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
getIndex() - Method in class htsjdk.samtools.SRAFileReader
 
getIndex(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Find the rank of the specified interval.

getIndexCreator() - Method in enum htsjdk.tribble.index.IndexFactory.IndexType
 
getIndexedFile() - Method in class htsjdk.tribble.index.AbstractIndex
 
getIndexedFileMD5() - Method in class htsjdk.tribble.index.AbstractIndex
 
getIndexedFileSize() - Method in class htsjdk.tribble.index.AbstractIndex
 
getIndexedFileTS() - Method in class htsjdk.tribble.index.AbstractIndex
 
getIndexEntries() - Method in class htsjdk.samtools.LinearIndex

Direct access to the array.

getIndexEntry(String) - Method in class htsjdk.samtools.reference.FastaSequenceIndex

Retrieve the index entry associated with the given contig.

getIndexingBin() - Method in interface htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
 
getIndexStart() - Method in class htsjdk.samtools.LinearIndex
 
getIndexStats(BAMFileReader) - Static method in class htsjdk.samtools.BAMIndexMetaData

Prints meta-data statistics from BAM index (.bai) file
 Statistics include count of aligned and unaligned reads for each reference sequence
 and a count of all records with no start coordinate

getIndexType() - Method in enum htsjdk.tribble.index.IndexFactory.IndexType
 
getIndexType(BufferedInputStream) - Static method in enum htsjdk.tribble.index.IndexFactory.IndexType
 
getInferredInsertSize() - Method in class htsjdk.samtools.SAMRecord
 
getInferredInsertSize() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getInfoHeaderLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
 
getInfoHeaderLines() - Method in class htsjdk.variant.vcf.VCFHeader

Returns the INFO HeaderLines in their original ordering

getInfoLine(String, boolean) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines

Returns the standard info line for ID.

getInfoLine(String) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines

Returns the standard info line for ID.

getInputFileName() - Method in class htsjdk.samtools.util.BinaryCodec
 
getInputStream() - Method in class htsjdk.samtools.util.BinaryCodec
 
getInsertedInRecord() - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
 
getInstance() - Static method in class htsjdk.samtools.CustomReaderFactory
 
getInstance() - Static method in class htsjdk.samtools.DefaultSAMRecordFactory
 
getInstance() - Static method in class htsjdk.samtools.seekablestream.SeekableStreamFactory
 
getInstance(Class<?>) - Static method in class htsjdk.samtools.util.Log

Get a Log instance to perform logging within the Class specified.

getIntegerAttribute(String) - Method in class htsjdk.samtools.SAMRecord

Get the tag value and attempt to coerce it into the requested type.

getIntersectionLength(Interval) - Method in class htsjdk.samtools.util.Interval
 
getIntervals() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
getIntervals() - Method in class htsjdk.samtools.util.IntervalList

Gets the set of intervals as held internally.

getIntervals() - Method in class htsjdk.tribble.index.interval.IntervalTree

Return all intervals in tree.

getIsoDate(Date) - Static method in class htsjdk.samtools.util.DateParser

Generate a ISO 8601 date

getIterator() - Method in class htsjdk.samtools.CRAMFileReader
 
getIterator(SAMFileSpan) - Method in class htsjdk.samtools.CRAMFileReader
 
getIterator() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
getIterator(SAMFileSpan) - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
getIterator() - Method in class htsjdk.samtools.SRAFileReader
 
getIterator(SAMFileSpan) - Method in class htsjdk.samtools.SRAFileReader
 
getKey() - Method in class htsjdk.samtools.cram.structure.ReadTag
 
getKey() - Method in class htsjdk.variant.vcf.VCFHeaderLine

Get the key

getKeyAndType() - Method in class htsjdk.samtools.cram.structure.ReadTag
 
getKeySequence() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getLabel() - Method in enum htsjdk.samtools.SAMFlag
 
getLandedRefMaskScores() - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
getLandedTotalScores() - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
getLastChunk() - Method in class htsjdk.samtools.Bin

Warning:  Currently only valid during index building, not when reading existing index,
 (AbstractBAMFileIndex.optimizeChunkList doesn't maintain this)

getLastCigarElement() - Method in class htsjdk.samtools.Cigar

returns the last cigar element

getLastLocusInBin(Bin) - Method in class htsjdk.samtools.AbstractBAMFileIndex

Gets the last locus that this bin can index into.

getLastLocusInBin(Bin) - Method in interface htsjdk.samtools.BrowseableBAMIndex

Gets the last locus that this bin can index into.

getLastLocusInBin(Bin) - Method in class htsjdk.samtools.SRAIndex

Gets the last locus that this bin can index into.

getLeftmost(List<CRAIEntry>) - Static method in class htsjdk.samtools.cram.CRAIIndex
 
getLength() - Method in class htsjdk.samtools.AlignmentBlock

The number of contiguous bases aligned to the reference.

getLength() - Method in class htsjdk.samtools.CigarElement
 
getLength() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
getLength() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
getLength() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
getLength() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
getLength() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
getLength(int, int) - Static method in class htsjdk.samtools.util.CoordMath
 
getLength() - Method in class htsjdk.samtools.util.IntervalTree.Node
 
getLevelForBin(Bin) - Method in class htsjdk.samtools.AbstractBAMFileIndex

Gets the level associated with the given bin number.

getLevelForBin(Bin) - Method in interface htsjdk.samtools.BrowseableBAMIndex

Gets the level associated with the given bin number.

getLevelForBin(Bin) - Method in class htsjdk.samtools.SRAIndex

SRA only operates on bins from last level

getLevelSize(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex

Gets the number of bins in the given level.

getLevelSize(int) - Method in interface htsjdk.samtools.BrowseableBAMIndex

Gets the size (number of bins in) a given level of a BAM index.

getLevelSize(int) - Method in class htsjdk.samtools.SRAIndex

Gets the size (number of bins in) a given level of a BAM index.

getLibrary() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getLiftOverMinMatch() - Method in class htsjdk.samtools.liftover.LiftOver

Get minimum fraction of bases that must remap.

getLikelihoods() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
getLikelihoods() - Method in class htsjdk.variant.variantcontext.Genotype

Returns the GenotypesLikelihoods data associated with this Genotype, or null if missing

getLikelihoodsString() - Method in class htsjdk.variant.variantcontext.Genotype

Convenience function that returns a string representation of the PL field of this
 genotype, or .

getLinearIndex() - Method in class htsjdk.samtools.BinningIndexContent
 
getLineNumber() - Method in class htsjdk.samtools.fastq.FastqReader
 
getLineNumber() - Method in class htsjdk.samtools.util.BufferedLineReader
 
getLineNumber() - Method in interface htsjdk.samtools.util.LineReader
 
getLineNumber() - Method in class htsjdk.samtools.util.StringLineReader
 
getLink() - Method in interface htsjdk.tribble.bed.BEDFeature
 
getLink() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getLODBestToNext() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
getLODBestToReference() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
getLog10GQ(GenotypeType) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

Deprecated.

getLog10GQ(Genotype, List<Allele>) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
getLog10GQ(Genotype, VariantContext) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
getLog10PError() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getLog10PError() - Method in class htsjdk.variant.variantcontext.Genotype

Deprecated.

getLog10PError() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getLongCrc32() - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
 
getMagicNumber() - Method in enum htsjdk.tribble.index.IndexFactory.IndexType
 
getMajorVersion() - Method in class htsjdk.variant.bcf2.BCFVersion
 
getMappingQuality() - Method in class htsjdk.samtools.SAMRecord
 
getMappingQuality() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getMappingQualityScoreCutoff() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
getMatchingAllele(Collection<Allele>, byte[]) - Static method in class htsjdk.variant.variantcontext.Allele
 
getMateAlignmentBlocks(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
 
getMateAlignmentEnd(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

This method uses the MateCigar value as determined from the attribute MC.

getMateAlignmentStart() - Method in class htsjdk.samtools.SAMRecord
 
getMateAlignmentStart() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getMateCigar(SAMRecord, boolean) - Static method in class htsjdk.samtools.SAMUtils

Returns the Mate Cigar or null if there is none.

getMateCigar(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Returns the Mate Cigar or null if there is none.

getMateCigarLength(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
 
getMateCigarString(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Returns the Mate Cigar String as stored in the attribute 'MC'.

getMateFlags() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
getMateNegativeStrandFlag() - Method in class htsjdk.samtools.SAMRecord

strand of the mate (false for forward; true for reverse strand).

getMateNegativeStrandFlag() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getMateReferenceIndex() - Method in class htsjdk.samtools.SAMRecord

Returns the mate reference index for this record.

getMateReferenceIndex() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getMateReferenceName() - Method in class htsjdk.samtools.SAMRecord
 
getMateReferenceName() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getMateUnclippedEnd(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
 
getMateUnclippedStart(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
 
getMateUnmappedFlag() - Method in class htsjdk.samtools.SAMRecord

the mate is unmapped.

getMateUnmappedFlag() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getMax() - Method in class htsjdk.samtools.util.Histogram

Returns the key with the highest count.

getMaxAddressibleGenomicLocation() - Method in class htsjdk.samtools.AbstractBAMFileIndex

Gets the possible number of bins for a given reference sequence.

getMaximumMappingQual() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
getMaxPloidy(int) - Method in class htsjdk.variant.variantcontext.GenotypesContext

What is the max ploidy among all samples?  Returns defaultPloidy if no genotypes are present

getMaxPloidy(int) - Method in class htsjdk.variant.variantcontext.VariantContext

Returns the maximum ploidy of all samples in this VC, or default if there are no genotypes

 This function is caching, so it's only expensive on the first call

getMaxPosition() - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask
 
getMaxPosition() - Method in interface htsjdk.samtools.util.ReferenceSequenceMask
 
getMaxPosition() - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
 
getMaxReadsToAccumulatePerLocus() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
getMaxSequenceIndex() - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask
 
getMaxSequenceIndex() - Method in interface htsjdk.samtools.util.ReferenceSequenceMask
 
getMaxSequenceIndex() - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
 
getMd5() - Method in exception htsjdk.samtools.cram.ref.EnaRefService.GaveUpException
 
getMd5() - Method in class htsjdk.samtools.SAMSequenceRecord
 
getMean() - Method in class htsjdk.samtools.util.Histogram

Assuming that the key type for the histogram is a Number type, returns the mean of
 all the items added to the histogram.

getMeanBinSize() - Method in class htsjdk.samtools.util.Histogram

Calculates the mean bin size

getMedian() - Method in class htsjdk.samtools.util.Histogram
 
getMedianAbsoluteDeviation() - Method in class htsjdk.samtools.util.Histogram

Gets the median absolute deviation of the distribution.

getMedianBinSize() - Method in class htsjdk.samtools.util.Histogram

Calculates the median bin size

getMergedHeader() - Method in class htsjdk.samtools.MergingSamRecordIterator

Returns the merged header that the merging iterator is working from.

getMergedHeader() - Method in class htsjdk.samtools.SamFileHeaderMerger

Returns the merged header that should be written to any output merged file.

getMergedSequenceIndex(SamReader, Integer) - Method in class htsjdk.samtools.SamFileHeaderMerger

Deprecated.
replaced by SamFileHeaderMerger.getMergedSequenceIndex(SAMFileHeader, Integer)


getMergedSequenceIndex(SAMFileHeader, Integer) - Method in class htsjdk.samtools.SamFileHeaderMerger

Another mechanism for getting the new sequence index, for situations in which the reader is not available.

getMessage() - Method in class htsjdk.samtools.SAMValidationError
 
getMessage() - Method in exception htsjdk.tribble.TribbleException

override the default message with ours, which attaches the source file in question

getMetaData(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex

Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records

getMetaData(int) - Method in interface htsjdk.samtools.BAMIndex

Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records

getMetaData(int) - Method in class htsjdk.samtools.SRAIndex
 
getMetaDataForField(VCFHeader, String) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
 
getMetaDataInInputOrder() - Method in class htsjdk.variant.vcf.VCFHeader

get the meta data, associated with this header, in sorted order

getMetaDataInSortedOrder() - Method in class htsjdk.variant.vcf.VCFHeader
 
getMetaDataLine(String) - Method in class htsjdk.variant.vcf.VCFHeader

Get the VCFHeaderLine whose key equals key.

getMethod() - Method in class htsjdk.samtools.cram.encoding.ExternalCompressor
 
getMetrics() - Method in class htsjdk.samtools.metrics.MetricsFile

Returns the list of headers.

getMetricsColumnLabels() - Method in class htsjdk.samtools.metrics.MetricsFile
 
getMin() - Method in class htsjdk.samtools.util.Histogram

Returns the key with the lowest count.

getMinimumOffset(int) - Method in class htsjdk.samtools.LinearIndex

Gets the minimum offset of any alignment start appearing in this index, according to the linear index.

getMinorVersion() - Method in class htsjdk.variant.bcf2.BCFVersion
 
getMinutes() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

getMissingBytes() - Method in enum htsjdk.variant.bcf2.BCF2Type

The bytes (encoded as an int) that are used to represent a missing value
 for this type in BCF2

getMissingJavaValue() - Method in enum htsjdk.variant.bcf2.BCF2Type

Return the java object (aka null) that is used to represent a missing value for this
 type in Java

getMixedCount() - Method in class htsjdk.variant.variantcontext.VariantContext

Genotype-specific functions -- how many mixed calls are there in the genotypes?

getMode() - Method in class htsjdk.samtools.util.Histogram

Returns id of the Bin that's the mode of the distribution (i.e.

getMonth() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

getNAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getName() - Method in class htsjdk.samtools.reference.ReferenceSequence

Gets the set of names given to this sequence in the source file.

getName() - Method in class htsjdk.samtools.util.Interval

Returns the name of the interval, possibly null.

getName() - Method in interface htsjdk.tribble.bed.BEDFeature
 
getName() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getName() - Method in interface htsjdk.tribble.index.ChrIndex
 
getName() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
 
getName() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
getName() - Method in interface htsjdk.tribble.NameAwareCodec
 
getName() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getName() - Method in class htsjdk.variant.vcf.AbstractVCFCodec

get the name of this codec

getNBlocks() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
getNext() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
 
getNFeatures() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
getNGenotypeSamples() - Method in class htsjdk.variant.vcf.VCFHeader
 
getNoCallCount() - Method in class htsjdk.variant.variantcontext.VariantContext

Genotype-specific functions -- how many no-calls are there in the genotypes?

getNoCoordinateCount() - Method in class htsjdk.samtools.AbstractBAMFileIndex

Returns count of records unassociated with any reference.

getNonCollidingId(String) - Method in class htsjdk.samtools.SAMFileHeader.PgIdGenerator
 
getNotPrimaryAlignmentFlag() - Method in class htsjdk.samtools.SAMRecord

the alignment is not primary (a read having split hits may have multiple primary alignment records).

getNotPrimaryAlignmentFlag() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getNSamples() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getNumAttributes() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
getNumber() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
 
getNumber() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
 
getNumberOfReads(ReadCollection) - Static method in class htsjdk.samtools.sra.SRAUtils

Is used to build RecordRangeInfo

getNumberOfReads() - Method in class htsjdk.samtools.SRAIterator.RecordRangeInfo
 
getNumberOfReferences() - Method in class htsjdk.samtools.AbstractBAMFileIndex
 
getNumHistograms() - Method in class htsjdk.samtools.metrics.MetricsFile

Returns the number of histograms added to the metrics file.

getNumIndexLevels() - Static method in class htsjdk.samtools.AbstractBAMFileIndex

Get the number of levels employed by this index.

getNumMateCigarsAdded() - Method in class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
 
getNumOverlappingAlignedBasesToClip(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Returns the number of bases that need to be clipped due to overlapping pairs.

getNumRecordsOnDisk() - Method in class htsjdk.samtools.util.DiskBackedQueue
 
getOffset() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
getOperator() - Method in class htsjdk.samtools.CigarElement
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
getOperator() - Method in interface htsjdk.samtools.cram.encoding.readfeatures.ReadFeature

Read features are distinguished by operator, similar to cigar operator.

getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
getOrElse(T, T) - Static method in class htsjdk.samtools.util.CodeUtil

Mimic of Oracle's nvl() - returns the first value if not null, otherwise the second value.

getOriginalBaseQualities() - Method in class htsjdk.samtools.SAMRecord

If the original base quality scores have been store in the "OQ" tag will return the numeric
 score as a byte[]

getOtherCanonicalAlignments(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Extract a List of 'other canonical alignments' from a SAM record.

getOtherHeaderLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
 
getOtherHeaderLines() - Method in class htsjdk.variant.vcf.VCFHeader

Returns the other HeaderLines in their original ordering

getOutputFileName() - Method in class htsjdk.samtools.util.BinaryCodec
 
getOutputStream() - Method in class htsjdk.samtools.util.BinaryCodec
 
getOverlap(int, int, int, int) - Static method in class htsjdk.samtools.util.CoordMath

Determines the amount of overlap between two coordinate ranges.

getOverlapping(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
getOverlaps(Locatable) - Method in class htsjdk.samtools.util.OverlapDetector

Gets the Set of objects that overlap the provided locatable.

getPaddedReferenceLength() - Method in class htsjdk.samtools.Cigar
 
getPairedReadName() - Method in class htsjdk.samtools.SAMRecord
 
getPairOrientation(SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil

Computes the pair orientation of the given SAMRecord.

getPartition(V) - Method in class htsjdk.samtools.util.CollectionUtil.Partitioner

Deprecated.
 
getPassword() - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
 
getPercentile(double) - Method in class htsjdk.samtools.util.Histogram

Gets the bin in which the given percentile falls.

getPhredScaledQual() - Method in class htsjdk.variant.variantcontext.CommonInfo

Floating-point arithmetic allows signed zeros such as +0.0 and -0.0.

getPhredScaledQual() - Method in class htsjdk.variant.variantcontext.Genotype

Deprecated.

getPhredScaledQual() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getPhredScoreFromErrorProbability(double) - Static method in class htsjdk.samtools.util.QualityUtil

Gets the phred score for any given probability of error.

getPhredScoreFromObsAndErrors(double, double) - Static method in class htsjdk.samtools.util.QualityUtil

Gets the phred score given the specified observations and errors.

getPL() - Method in class htsjdk.variant.variantcontext.FastGenotype
 
getPL() - Method in class htsjdk.variant.variantcontext.Genotype

Unsafe low-level accessor the PL field itself, may be null.

getPlatform() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getPlatformModel() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getPlatformUnit() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getPLIndecesOfAlleles(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

get the PL indexes (AA, AB, BB) for the given allele pair; assumes allele1Index <= allele2Index.

getPloidy() - Method in class htsjdk.variant.variantcontext.Genotype

What is the ploidy of this sample?

getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
getPosition() - Method in interface htsjdk.samtools.cram.encoding.readfeatures.ReadFeature
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
getPosition() - Method in class htsjdk.samtools.util.AbstractLocusInfo
 
getPosition() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
 
getPosition() - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
 
getPosition() - Method in interface htsjdk.samtools.util.LocationAware

The current offset, in bytes, of this stream/writer/file.

getPosition() - Method in interface htsjdk.samtools.util.Locus
 
getPosition() - Method in class htsjdk.samtools.util.LocusImpl
 
getPosition() - Method in class htsjdk.samtools.util.PositionalOutputStream
 
getPosition() - Method in class htsjdk.tribble.readers.AsciiLineReader
 
getPosition() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator

Returns the byte position at the end of the most-recently-read line (a.k.a., the beginning of the next line) from AsciiLineReaderIterator.next() in
 the underlying AsciiLineReader.

getPosition() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
 
getPredictedMedianInsertSize() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getPreservationPolicies() - Method in class htsjdk.samtools.cram.lossy.QualityScorePreservation
 
getPreservationPolicies() - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
getPreservationPolicies() - Method in class htsjdk.samtools.CRAMFileWriter
 
getPreviousProgramGroupId() - Method in class htsjdk.samtools.SAMProgramRecord
 
getPreviousRecord() - Method in class htsjdk.samtools.SAMSortOrderChecker
 
getProgramGroup() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getProgramGroupId(SamReader, String) - Method in class htsjdk.samtools.SamFileHeaderMerger

Deprecated.
replaced by SamFileHeaderMerger.getProgramGroupId(SAMFileHeader, String)


getProgramGroupId(SAMFileHeader, String) - Method in class htsjdk.samtools.SamFileHeaderMerger
 
getProgramGroupId() - Method in class htsjdk.samtools.SAMProgramRecord
 
getProgramName() - Method in class htsjdk.samtools.SAMProgramRecord
 
getProgramRecord(String) - Method in class htsjdk.samtools.SAMFileHeader
 
getProgramRecords() - Method in class htsjdk.samtools.SAMFileHeader
 
getProgramVersion() - Method in class htsjdk.samtools.SAMProgramRecord
 
getProperPairFlag() - Method in class htsjdk.samtools.SAMRecord

the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).

getProperPairFlag() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getProperties() - Method in class htsjdk.tribble.index.AbstractIndex

return a mapping of name to property value

getProperties() - Method in interface htsjdk.tribble.index.Index
 
getProperties() - Method in class htsjdk.tribble.index.tabix.TabixIndex

No arbitrary properties in Tabix

getQualityScore() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
 
getQualityScore() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
getQualityScoreCutoff() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
getQueryResults(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
 
getQueryResults(int) - Method in class htsjdk.samtools.DiskBasedBAMFileIndex
 
getRawContent() - Method in class htsjdk.samtools.cram.structure.Block
 
getRawContentSize() - Method in class htsjdk.samtools.cram.structure.Block
 
getReadBase() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
getReadBases() - Method in class htsjdk.samtools.BAMRecord
 
getReadBases() - Method in class htsjdk.samtools.SAMRecord

Do not modify the value returned by this method.

getReadBases() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getReader() - Method in class htsjdk.samtools.SAMFileSource

Retrieves the reader from which this read was initially retrieved.

getReaders() - Method in class htsjdk.samtools.SamFileHeaderMerger

Deprecated.
replaced by SamFileHeaderMerger.getHeaders()


getReadFailsVendorQualityCheckFlag() - Method in class htsjdk.samtools.SAMRecord

the read fails platform/vendor quality checks.

getReadGroup(String) - Method in class htsjdk.samtools.SAMFileHeader

Look up read group record by name.

getReadGroup() - Method in class htsjdk.samtools.SAMRecord

Get the SAMReadGroupRecord for this SAMRecord.

getReadGroupId(SamReader, String) - Method in class htsjdk.samtools.SamFileHeaderMerger

Deprecated.
replaced by SamFileHeaderMerger.getReadGroupId(SAMFileHeader, String)


getReadGroupId(SAMFileHeader, String) - Method in class htsjdk.samtools.SamFileHeaderMerger

Returns the read group id that should be used for the input read and RG id.

getReadGroupId() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getReadGroupMap() - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
getReadGroups() - Method in class htsjdk.samtools.SAMFileHeader
 
getReadHeader() - Method in class htsjdk.samtools.fastq.FastqRecord
 
getReadLength() - Method in class htsjdk.samtools.BAMRecord

Avoids decoding binary block to get read length.

getReadLength() - Method in class htsjdk.samtools.Cigar
 
getReadLength(List<CigarElement>) - Static method in class htsjdk.samtools.Cigar
 
getReadLength() - Method in class htsjdk.samtools.SAMRecord

This method is preferred over getReadBases().length, because for BAMRecord it may be faster.

getReadName() - Method in class htsjdk.samtools.BAMRecord
 
getReadName() - Method in class htsjdk.samtools.SAMRecord
 
getReadName() - Method in class htsjdk.samtools.SAMValidationError

may be null

getReadName() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
getReadNameLength() - Method in class htsjdk.samtools.BAMRecord

Avoids decoding read name to get read name length.

getReadNameLength() - Method in class htsjdk.samtools.SAMRecord

This method is preferred over getReadName().length(), because for BAMRecord
 it may be faster.

getReadNegativeStrandFlag() - Method in class htsjdk.samtools.SAMRecord

strand of the query (false for forward; true for reverse strand).

getReadNegativeStrandFlag() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getReadPairedFlag() - Method in class htsjdk.samtools.SAMRecord

the read is paired in sequencing, no matter whether it is mapped in a pair.

getReadPairedFlag() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getReadPositionAtReferencePosition(int) - Method in class htsjdk.samtools.SAMRecord
 
getReadPositionAtReferencePosition(int, boolean) - Method in class htsjdk.samtools.SAMRecord
 
getReadPositionAtReferencePosition(SAMRecord, int, boolean) - Static method in class htsjdk.samtools.SAMRecord
 
getReadStart() - Method in class htsjdk.samtools.AlignmentBlock

The first, 1-based, base in the read that is aligned to the reference reference.

getReadString() - Method in class htsjdk.samtools.fastq.FastqRecord
 
getReadString() - Method in class htsjdk.samtools.SAMRecord
 
getReadUnmappedFlag() - Method in class htsjdk.samtools.SAMRecord

the query sequence itself is unmapped.

getRecord() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
getRecord() - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
 
getRecordAndOffsets() - Method in class htsjdk.samtools.util.AbstractLocusInfo
 
getRecordAndPositions() - Method in class htsjdk.samtools.util.AbstractLocusInfo

Deprecated.
since name of the method can be confusing, new implementation should be used
          getRecordAndOffsets()


getRecordBytes() - Method in class htsjdk.variant.bcf2.BCF2Decoder

Returns the byte[] for the block of data we are currently decoding

getRecordBytes() - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
getRecordKey() - Method in class htsjdk.samtools.filter.AbstractJavascriptFilter

returns key used for record binding

getRecordKey() - Method in class htsjdk.samtools.filter.JavascriptSamRecordFilter
 
getRecordKey() - Method in class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter
 
getRecordNumber() - Method in class htsjdk.samtools.SAMValidationError

1-based.

getRecordOrdinal() - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
 
getRecords(Container, ArrayList<CramCompressionRecord>, ValidationStringency) - Method in class htsjdk.samtools.cram.build.ContainerParser
 
getRecords(boolean) - Method in class htsjdk.samtools.DuplicateSet

Gets the list of records from this set.

getRecords() - Method in class htsjdk.samtools.DuplicateSet

Gets the list of records from this set.

getRecords() - Method in class htsjdk.samtools.SAMRecordSetBuilder

Returns the accumulated list of sam records.

getRecordsRangeInfo() - Method in class htsjdk.samtools.SRAFileReader
 
getRecordsRangeInfo(ReadCollection) - Static method in class htsjdk.samtools.SRAIterator

Loads record ranges needed for emulating BAM index

getRefBase() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
 
getRefBases() - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
getReference() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getReferenceBase() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
getReferenceBases(SAMSequenceRecord, boolean) - Method in interface htsjdk.samtools.cram.ref.CRAMReferenceSource

getReferenceBases

getReferenceBases(SAMSequenceRecord, boolean) - Method in class htsjdk.samtools.cram.ref.ReferenceSource
 
getReferenceIndex() - Method in class htsjdk.samtools.SAMRecord

Returns the reference index for this record.

getReferenceIndex() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getReferenceLength() - Method in class htsjdk.samtools.Cigar
 
getReferenceLength() - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
 
getReferenceLength() - Method in class htsjdk.samtools.SAMSequenceDictionary
 
getReferenceLengthsAligned() - Method in class htsjdk.samtools.SRAIterator.RecordRangeInfo
 
getReferenceName() - Method in class htsjdk.samtools.SAMRecord
 
getReferenceName() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getReferenceOffsets() - Method in class htsjdk.samtools.SRAIterator.RecordRangeInfo
 
getReferencePositionAtReadPosition(int) - Method in class htsjdk.samtools.SAMRecord
 
getReferencePositionAtReadPosition(SAMRecord, int) - Static method in class htsjdk.samtools.SAMRecord
 
getReferences(Container, ValidationStringency) - Method in class htsjdk.samtools.cram.build.ContainerParser
 
getReferenceSequence() - Method in class htsjdk.samtools.Bin
 
getReferenceSequence() - Method in class htsjdk.samtools.BinList

Get the reference sequence to which this bin belongs.

getReferenceSequence() - Method in class htsjdk.samtools.BinningIndexContent

Reference for this Content

getReferenceSequence() - Method in class htsjdk.samtools.LinearIndex
 
getReferenceSequence(int) - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
getReferenceSequenceFile(File) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory

Attempts to determine the type of the reference file and return an instance
 of ReferenceSequenceFile that is appropriate to read it.

getReferenceSequenceFile(File, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory

Attempts to determine the type of the reference file and return an instance
 of ReferenceSequenceFile that is appropriate to read it.

getReferenceSequenceFile(File, boolean, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory

Attempts to determine the type of the reference file and return an instance
 of ReferenceSequenceFile that is appropriate to read it.

getReferenceSequenceFile(Path) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory

Attempts to determine the type of the reference file and return an instance
 of ReferenceSequenceFile that is appropriate to read it.

getReferenceSequenceFile(Path, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory

Attempts to determine the type of the reference file and return an instance
 of ReferenceSequenceFile that is appropriate to read it.

getReferenceSequenceFile(Path, boolean, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory

Attempts to determine the type of the reference file and return an instance
 of ReferenceSequenceFile that is appropriate to read it.

getReferencesLengthsAligned(ReadCollection) - Static method in class htsjdk.samtools.sra.SRAUtils

Loads reference lengths from a read collection.

getReferenceSpans() - Method in class htsjdk.samtools.cram.encoding.reader.RefSeqIdReader
 
getReferenceStart() - Method in class htsjdk.samtools.AlignmentBlock

The first, 1-based, position in the reference to which the read is aligned.

getRefPos() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
getRefSNPs() - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
getRelationship(IntervalTree.Node<V1>) - Method in class htsjdk.samtools.util.IntervalTree.Node
 
getReply() - Method in class htsjdk.samtools.util.ftp.FTPClient
 
getReplyString() - Method in class htsjdk.samtools.util.ftp.FTPReply

Gets server reply string from the control port after an ftp command has
 been executed.

getRepresentative() - Method in class htsjdk.samtools.DuplicateSet

Gets the representative record according to the duplicate comparator.

getResourceDescription() - Method in interface htsjdk.samtools.SamReader
 
getResourceDescription() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
getRunDate() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getSamFileHeader() - Method in class htsjdk.samtools.cram.structure.CramHeader

Get the SAMFileHeader object associated with this CRAM file header.

getSAMFileHeader() - Method in class htsjdk.samtools.CRAMIterator
 
getSAMFlags() - Method in class htsjdk.samtools.SAMRecord

shortcut to

getSample() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getSampleName() - Method in class htsjdk.variant.variantcontext.Genotype

Returns the name associated with this sample.

getSampleNames() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
getSampleNames() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getSampleNamesInOrder() - Method in class htsjdk.variant.vcf.VCFHeader
 
getSampleNamesOrderedByName() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
getSampleNamesOrderedByName() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getSampleNameToOffset() - Method in class htsjdk.variant.vcf.VCFHeader
 
getSamReader() - Method in class htsjdk.samtools.SAMRecordSetBuilder

Creates samFileReader from the data in instance of this class

getSamReadNameFromFastqHeader(String) - Static method in class htsjdk.samtools.util.SequenceUtil

Returns a read name from a FASTQ header string suitable for use in a SAM/BAM file.

getSAMSequenceRecord() - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
 
getSAMString() - Method in class htsjdk.samtools.SAMRecord

Returns the record in the SAM line-based text format.

getScore() - Method in interface htsjdk.tribble.bed.BEDFeature
 
getScore() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getScores() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
getSecondOfPairFlag() - Method in class htsjdk.samtools.SAMRecord

the read is the second read in a pair.

getSecondOfPairFlag() - Method in class htsjdk.samtools.sra.SRALazyRecord
 
getSeconds() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

getSeenCount() - Method in class htsjdk.samtools.DownsamplingIterator

Returns the number of records seen, including accepted and discarded, since creation of the last call to resetStatistics.

getSentinel() - Method in class htsjdk.samtools.util.IntervalTree

Get the special sentinel value that will be used to signal novelty when putting a new interval
 into the tree, or to signal "not found" when removing an interval.

getSequence() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
getSequence() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
getSequence(String) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile

Retrieves the complete sequence described by this contig.

getSequence(String) - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile

Retrieves the complete sequence described by this contig.

getSequence(String) - Method in class htsjdk.samtools.SAMFileHeader

Look up sequence record by name.

getSequence(int) - Method in class htsjdk.samtools.SAMFileHeader

Look up a sequence record by index.

getSequence(String) - Method in class htsjdk.samtools.SAMSequenceDictionary
 
getSequence(int) - Method in class htsjdk.samtools.SAMSequenceDictionary
 
getSequence(String) - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
getSequence() - Method in class htsjdk.samtools.util.Interval

Deprecated.
use getContig() instead


getSequenceDictionary() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile

Retrieves the sequence dictionary for the fasta file.

getSequenceDictionary() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile

Must return a sequence dictionary with at least the following fields completed
 for each sequence: name, length.

getSequenceDictionary() - Method in class htsjdk.samtools.reference.ReferenceSequenceFileWalker
 
getSequenceDictionary() - Method in class htsjdk.samtools.SAMFileHeader
 
getSequenceDictionary() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
getSequenceDictionary(File) - Static method in class htsjdk.tribble.util.TabixUtils

Generates the SAMSequenceDictionary from the given tabix index file

getSequenceDictionary(File) - Static method in class htsjdk.variant.vcf.VCFFileReader

Returns the SAMSequenceDictionary from the provided VCF file.

getSequenceDictionary() - Method in class htsjdk.variant.vcf.VCFHeader

Returns the contigs in this VCF file as a SAMSequenceDictionary.

getSequenceId() - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
 
getSequenceIndex(String) - Method in class htsjdk.samtools.SAMFileHeader
 
getSequenceIndex(String) - Method in class htsjdk.samtools.SAMSequenceDictionary
 
getSequenceIndex() - Method in class htsjdk.samtools.SAMSequenceRecord
 
getSequenceIndex() - Method in class htsjdk.samtools.util.AbstractLocusInfo
 
getSequenceIndex() - Method in interface htsjdk.samtools.util.Locus
 
getSequenceIndex() - Method in class htsjdk.samtools.util.LocusImpl
 
getSequenceLength() - Method in class htsjdk.samtools.SAMSequenceRecord
 
getSequenceLength() - Method in class htsjdk.samtools.util.AbstractLocusInfo
 
getSequenceName() - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
 
getSequenceName() - Method in class htsjdk.samtools.SAMSequenceRecord
 
getSequenceName() - Method in class htsjdk.samtools.util.AbstractLocusInfo
 
getSequenceNameList(SAMSequenceDictionary) - Static method in class htsjdk.variant.variantcontext.VariantContextComparator
 
getSequenceNames() - Method in interface htsjdk.tribble.FeatureReader
 
getSequenceNames() - Method in class htsjdk.tribble.index.AbstractIndex
 
getSequenceNames() - Method in interface htsjdk.tribble.index.Index
 
getSequenceNames() - Method in class htsjdk.tribble.index.linear.LinearIndex
 
getSequenceNames() - Method in class htsjdk.tribble.index.tabix.TabixIndex
 
getSequenceNames() - Method in class htsjdk.tribble.TabixFeatureReader
 
getSequenceNames() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader

Return the sequence (chromosome/contig) names in this file, if known.

getSequences() - Method in class htsjdk.samtools.SAMSequenceDictionary
 
getSequencingCenter() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
getShortAttribute(String) - Method in class htsjdk.samtools.SAMRecord

Get the tag value and attempt to coerce it into the requested type.

getSignedByteArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord

Will work for signed byte array or old-style hex array

getSignedIntArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getSignedShortArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getSingleChunk() - Method in class htsjdk.samtools.BAMFileSpan

Checks that there is only a single chunk for this span and returns it.

getSingleton() - Static method in class htsjdk.samtools.SAMTagUtil

Despite the fact that this class has state, it should be thread-safe because the cache
 gets filled with the same values by any thread.

getSingleton() - Static method in class htsjdk.samtools.util.SolexaQualityConverter
 
getSiteFieldWriter(String) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager

Get a site writer specialized to encode values for site info field

getSize() - Method in class htsjdk.tribble.index.Block
 
getSize() - Method in class htsjdk.tribble.index.interval.IntervalTree

The estimated size of the tree.

getSize(VariantContext) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
 
getSize(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.Accessor
 
getSizeInBytes() - Method in enum htsjdk.variant.bcf2.BCF2Type

How many bytes are used to represent this type on disk?

getSoleElement(Collection<T>) - Static method in class htsjdk.samtools.util.CollectionUtil
 
getSolexaToPhredConversionTable() - Method in class htsjdk.samtools.util.SolexaQualityConverter
 
getSortKey(SAMRecord) - Method in class htsjdk.samtools.SAMSortOrderChecker

Return the sort key used for the given sort order.

getSortOrder() - Method in class htsjdk.samtools.SAMFileHeader
 
getSortOrder() - Method in class htsjdk.samtools.SAMFileWriterImpl

Must be called after calling setHeader().

getSource() - Method in class htsjdk.samtools.SAMValidationError
 
getSource() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
 
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
 
getSource() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
 
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableStream
 
getSource() - Method in class htsjdk.tribble.readers.TabixReader

return the source (filename/URL) of that reader

getSource() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getSpan() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
 
getSpanOverlapping(int, int, int) - Method in interface htsjdk.samtools.BAMIndex

Gets the compressed chunks which should be searched for the contents of records contained by the span
 referenceIndex:startPos-endPos, inclusive.

getSpanOverlapping(Bin) - Method in interface htsjdk.samtools.BrowseableBAMIndex

Perform an overlapping query of all bins bounding the given location.

getSpanOverlapping(int, int, int) - Method in class htsjdk.samtools.DiskBasedBAMFileIndex

Get list of regions of BAM file that may contain SAMRecords for the given range

getSpanOverlapping(Bin) - Method in class htsjdk.samtools.SRAIndex
 
getSpanOverlapping(int, int, int) - Method in class htsjdk.samtools.SRAIndex
 
getSpecies() - Method in class htsjdk.samtools.SAMSequenceRecord
 
getStandardDeviation() - Method in class htsjdk.samtools.util.Histogram
 
getStandardDeviationBinSize(double) - Method in class htsjdk.samtools.util.Histogram

Calculates the standard deviation of the bin size

getStart() - Method in interface htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
 
getStart() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
 
getStart() - Method in class htsjdk.samtools.SAMRecord

an alias of {@link #getAlignmentStart()

getStart(int, int) - Static method in class htsjdk.samtools.util.CoordMath
 
getStart() - Method in class htsjdk.samtools.util.EdgingRecordAndOffset
 
getStart() - Method in class htsjdk.samtools.util.Interval
 
getStart() - Method in class htsjdk.samtools.util.IntervalTree.Node
 
getStart() - Method in interface htsjdk.samtools.util.Locatable
 
getStart() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getStart() - Method in class htsjdk.tribble.gelitext.GeliTextFeature

Deprecated.
Return the start position in 1-based coordinates (first base is 1)

getStart() - Method in class htsjdk.tribble.SimpleFeature
 
getStart() - Method in class htsjdk.variant.variantcontext.VariantContext
 
getStartOffset() - Method in class htsjdk.tribble.bed.BEDCodec
 
getStartOfLastLinearBin() - Method in class htsjdk.samtools.AbstractBAMFileIndex

Use to get close to the unmapped reads at the end of a BAM file.

getStartOfLastLinearBin() - Method in interface htsjdk.samtools.BAMIndex

Gets the start of the last linear bin in the index.

getStartOfLastLinearBin() - Method in class htsjdk.samtools.SRAIndex
 
getStartPosition() - Method in class htsjdk.tribble.index.Block
 
getStaticType() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
getStats(CramRecordReader) - Method in class htsjdk.samtools.cram.encoding.reader.DataReaderFactory
 
getStrand() - Method in interface htsjdk.tribble.bed.BEDFeature
 
getStrand() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getStreamFor(URL) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory
 
getStreamFor(String) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory
 
getStringAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getStructuralVariantType() - Method in class htsjdk.variant.variantcontext.VariantContext

Search for the INFO=SVTYPE and return the type of Structural Variant

getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile

Gets the subsequence of the contig in the range [start,stop]

getSubsequenceAt(String, long, long) - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile

Gets the subsequence of the contig in the range [start,stop]

getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
getSum() - Method in class htsjdk.samtools.util.Histogram

Returns the sum of the products of the histgram bin ids and the number of entries in each bin.

getSumOfValues() - Method in class htsjdk.samtools.util.Histogram

Returns the sum of the number of entries in each bin.

getSupplementaryAlignmentFlag() - Method in class htsjdk.samtools.SAMRecord

the alignment is supplementary (TODO: further explanation?).

getTabixFormat() - Method in class htsjdk.tribble.bed.BEDCodec
 
getTabixFormat() - Method in class htsjdk.tribble.BinaryFeatureCodec

Marked as final because binary features could not be tabix indexed

getTabixFormat() - Method in interface htsjdk.tribble.FeatureCodec

Define the tabix format for the feature, used for indexing.

getTabixFormat() - Method in class htsjdk.variant.vcf.AbstractVCFCodec
 
getTagIds(int) - Method in class htsjdk.samtools.cram.structure.CompressionHeader
 
getTargetProportion() - Method in class htsjdk.samtools.DownsamplingIterator

Gets the target proportion of records that should be retained during downsampling.

getTempDirecory(String, String) - Static method in class htsjdk.samtools.util.TestUtil

Deprecated.
Use properly spelled method. TestUtil.getTempDirectory(java.lang.String, java.lang.String)


getTempDirectory(String, String) - Static method in class htsjdk.samtools.util.TestUtil
 
getTextHeader() - Method in class htsjdk.samtools.SAMFileHeader

If this SAMHeader was read from a file, this property contains the header
 as it appeared in the file, otherwise it is null.

getThreadNamePrefix() - Method in class htsjdk.samtools.fastq.AsyncFastqWriter
 
getThreadNamePrefix() - Method in class htsjdk.samtools.util.AbstractAsyncWriter

Returns the prefix to use when naming threads.

getThreadNamePrefix() - Method in class htsjdk.samtools.util.AsyncBufferedIterator
 
getThreadNamePrefix() - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
 
getTime() - Method in class htsjdk.samtools.util.RelativeIso8601Date
 
getTimestamp() - Method in class htsjdk.samtools.util.Log

Creates a date string for insertion into the log.

getTimezoneOffset() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

getTotalRecordRangeLength() - Method in class htsjdk.samtools.SRAIterator.RecordRangeInfo
 
getTotalReferencesLength() - Method in class htsjdk.samtools.SRAIterator.RecordRangeInfo
 
getTotalSize() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
getTransientAttribute(Object) - Method in class htsjdk.samtools.SAMRecord

Fetches the value of a transient attribute on the SAMRecord, of null if not set.

getTribbleIndexType() - Method in enum htsjdk.tribble.index.IndexFactory.IndexType
 
getType() - Method in class htsjdk.samtools.SAMValidationError
 
getType() - Method in class htsjdk.samtools.util.EdgingRecordAndOffset
 
getType() - Method in interface htsjdk.tribble.bed.BEDFeature
 
getType() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
getType() - Method in class htsjdk.tribble.index.AbstractIndex

get the index type

getType() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
 
getType() - Method in class htsjdk.tribble.index.linear.LinearIndex
 
getType() - Method in class htsjdk.variant.variantcontext.Genotype
 
getType() - Method in class htsjdk.variant.variantcontext.VariantContext

Determines (if necessary) and returns the type of this variation by examining the alleles it contains.

getType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

Get the BCF2 type for this field, either from the static type of the
 field itself or by inspecting the value itself.

getType() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
getUnalignedRecordCount() - Method in class htsjdk.samtools.BAMIndexMetaData
 
getUnclippedEnd() - Method in class htsjdk.samtools.SAMRecord
 
getUnclippedEnd(int, Cigar) - Static method in class htsjdk.samtools.SAMUtils
 
getUnclippedStart() - Method in class htsjdk.samtools.SAMRecord
 
getUnclippedStart(int, Cigar) - Static method in class htsjdk.samtools.SAMUtils
 
getUnderlyingIterator() - Method in class htsjdk.samtools.util.PeekIterator
 
getUniqueBaseCount() - Method in class htsjdk.samtools.util.IntervalList

Gets the count of unique bases represented by the intervals in the list.

getUniqueIntervals() - Method in class htsjdk.samtools.util.IntervalList

Deprecated.
use #uniqued()#getIntervals() instead.


getUniqueIntervals(IntervalList, boolean) - Static method in class htsjdk.samtools.util.IntervalList

Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()

getUniqueIntervals(IntervalList, boolean, boolean) - Static method in class htsjdk.samtools.util.IntervalList

Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()

getUniqueIntervals(boolean) - Method in class htsjdk.samtools.util.IntervalList

Deprecated.
use #uniqued(boolean)#getIntervals() or IntervalList.getUniqueIntervals(IntervalList, boolean) instead.


getUnparsedGenotypeData() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
 
getUnsignedByteArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getUnsignedIntArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getUnsignedIntegerAttribute(String) - Method in class htsjdk.samtools.SAMRecord

A convenience method that will return a valid unsigned integer as a Long,
 or fail with an exception if the tag value is invalid.

getUnsignedIntegerAttribute(short) - Method in class htsjdk.samtools.SAMRecord

A convenience method that will return a valid unsigned integer as a Long,
 or fail with an exception if the tag value is invalid.

getUnsignedShortArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
getUrl() - Method in class htsjdk.tribble.util.FTPHelper
 
getUrl() - Method in class htsjdk.tribble.util.HTTPHelper
 
getUrl() - Method in class htsjdk.tribble.util.RemoteURLHelper
 
getUrl() - Method in interface htsjdk.tribble.util.URLHelper
 
getURLHelper(URL) - Static method in class htsjdk.tribble.util.ParsingUtils

Return the registered URLHelper, constructed with the provided URL

getUser() - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
 
getValidationErrors() - Method in class htsjdk.samtools.SAMFileHeader
 
getValidationStringency() - Method in class htsjdk.samtools.CRAMFileReader
 
getValidationStringency() - Method in class htsjdk.samtools.CRAMIterator
 
getValidationStringency() - Method in class htsjdk.samtools.SAMLineParser

Get validation stringency.

getValidationStringency() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
getValidationStringency() - Method in class htsjdk.samtools.SAMRecord
 
getValidationStringency() - Method in class htsjdk.samtools.SRAFileReader
 
getValue() - Method in class htsjdk.samtools.cram.structure.ReadTag
 
getValue() - Method in class htsjdk.samtools.metrics.StringHeader
 
getValue() - Method in class htsjdk.samtools.util.Histogram.Bin

Gets the value in the bin.

getValue() - Method in class htsjdk.samtools.util.IntervalTree.Node
 
getValue(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.DPAccessor
 
getValue(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.GQAccessor
 
getValue() - Method in class htsjdk.variant.vcf.VCFHeaderLine

Get the value

getValueAsByteArray() - Method in class htsjdk.samtools.cram.structure.ReadTag
 
getValueLabel() - Method in class htsjdk.samtools.util.Histogram
 
getValues(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.Accessor
 
getValues(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.ADAccessor
 
getValues(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.PLAccessor
 
getValuesAndBitLengths(List<T>, List<Integer>, HuffmanTree<T>) - Static method in class htsjdk.samtools.cram.encoding.huffman.HuffmanCode
 
getValueString(double) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
 
getValueString(double) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Method description

getVariableBinaryRepresentation() - Method in class htsjdk.samtools.BAMRecord

If this record has a valid binary representation of the variable-length portion of a binary record stored,
 return that byte array, otherwise return null.

getVariableBinaryRepresentation() - Method in class htsjdk.samtools.SAMRecord

If this record has a valid binary representation of the variable-length portion of a binary record stored,
 return that byte array, otherwise return null.

getVCFRecordComparator() - Method in class htsjdk.variant.vcf.VCFHeader
 
getVersion() - Method in class htsjdk.samtools.cram.structure.CramHeader
 
getVersion() - Method in class htsjdk.samtools.SAMFileHeader
 
getVersion() - Method in class htsjdk.tribble.index.AbstractIndex
 
getVersionedItem() - Method in class htsjdk.samtools.metrics.VersionHeader
 
getVersionString() - Method in class htsjdk.samtools.metrics.VersionHeader
 
getVersionString() - Method in enum htsjdk.variant.vcf.VCFHeaderVersion
 
getWindowLength() - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
 
getWindowPosition() - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
 
getWriter() - Method in class htsjdk.samtools.SAMTextWriter

Returns the Writer used by this instance.

getWriter(String, Map<String, T>) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
 
getWrittenCount() - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
getYear() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

GFF - Static variable in class htsjdk.tribble.index.tabix.TabixFormat

Predefined headers for known formats

globalRecordCounter - Variable in class htsjdk.samtools.cram.structure.Container
 
globalRecordCounter - Variable in class htsjdk.samtools.cram.structure.Slice
 
GolombIntegerEncoding - Class in htsjdk.samtools.cram.encoding
 
GolombIntegerEncoding() - Constructor for class htsjdk.samtools.cram.encoding.GolombIntegerEncoding
 
GolombLongEncoding - Class in htsjdk.samtools.cram.encoding
 
GolombLongEncoding() - Constructor for class htsjdk.samtools.cram.encoding.GolombLongEncoding
 
GolombRiceIntegerEncoding - Class in htsjdk.samtools.cram.encoding
 
GolombRiceIntegerEncoding() - Constructor for class htsjdk.samtools.cram.encoding.GolombRiceIntegerEncoding
 
GQ(int) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
 
GQAccessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.GQAccessor
 
GROUP_ORDER_TAG - Static variable in class htsjdk.samtools.SAMFileHeader
 
GTWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GTWriter
 
gunzip(byte[]) - Static method in class htsjdk.samtools.cram.io.ExternalCompression

Uncompress a GZIP data blob into a new byte array.

gzip(byte[]) - Static method in class htsjdk.samtools.cram.io.ExternalCompression

Compress a byte array into GZIP blob.

GZIP_BLOCK_PREAMBLE - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
GZIP_CM_DEFLATE - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
GZIP_FLG - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
GZIP_ID1 - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
GZIP_ID2 - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
GZIP_OS_UNKNOWN - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
GZIP_OVERHEAD - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
GZIP_XFL - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
GZIP_XLEN - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 




H

H0 - Variable in class htsjdk.samtools.SAMTagUtil
 
H1 - Variable in class htsjdk.samtools.SAMTagUtil
 
H2 - Variable in class htsjdk.samtools.SAMTagUtil
 
hammingDistance(String, String) - Static method in class htsjdk.samtools.util.StringUtil

Calculates the Hamming distance (number of character mismatches) between two strings s1 and s2.

HAPLOTYPE_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
HAPMAP2_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
HAPMAP3_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
HARD_CLIP - Static variable in enum htsjdk.samtools.CigarOperator
 
HardClip - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing a hard clip similar to CigarOperator.H.

HardClip() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
HardClip(int, int) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
hardClipCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
hardClipCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
HardyWeinbergCalculation - Class in htsjdk.tribble.util.popgen

This class calculates a HardyWeinberg p-value given three values representing
 the observed frequences of homozygous and heterozygous genotypes in the
 test population.

HAS_GREATER_PART - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
HAS_LESSER_PART - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
HAS_OVERLAPPING_PART - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
hasAD() - Method in class htsjdk.variant.variantcontext.Genotype

Does the AD field have a value?

hasAllele(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasAllele(Allele, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasAlternateAllele(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasAlternateAllele(Allele, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasAnyAttribute(String) - Method in class htsjdk.variant.variantcontext.Genotype
 
hasAttribute(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
hasAttribute(String) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasBlockCompressedExtension(String) - Static method in class htsjdk.tribble.AbstractFeatureReader

Whether a filename ends in one of the BLOCK_COMPRESSED_EXTENSIONS

hasBlockCompressedExtension(File) - Static method in class htsjdk.tribble.AbstractFeatureReader

Whether the name of a file ends in one of the BLOCK_COMPRESSED_EXTENSIONS

hasBlockCompressedExtension(URI) - Static method in class htsjdk.tribble.AbstractFeatureReader

Whether the path of a URI resource ends in one of the BLOCK_COMPRESSED_EXTENSIONS

hasBrowseableIndex() - Method in class htsjdk.samtools.CRAMFileReader
 
hasBrowseableIndex() - Method in interface htsjdk.samtools.SamReader.Indexing

Returns true if the supported index is browseable, meaning the bins in it can be traversed
 and chunk data inspected and retrieved.

hasBrowseableIndex() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
hasBrowseableIndex() - Method in class htsjdk.samtools.SRAFileReader

Returns true if the supported index is browseable, meaning the bins in it can be traversed
 and chunk data inspected and retrieved.

hasConstantNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
hasConstantNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
 
hasContextDeterminedNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
hasContextDeterminedNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
 
hasCurrent() - Method in class htsjdk.samtools.NotPrimarySkippingIterator
 
hasCurrent() - Method in class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
 
hasDP() - Method in class htsjdk.variant.variantcontext.Genotype

Does the DP field have a value?

hasExtendedAttribute(String) - Method in class htsjdk.variant.variantcontext.Genotype

Is key associated with a value (even a null one) in the extended attributes?

 Note this will not return true for the inline attributes DP, GQ, AD, or PL

hasFileSize() - Method in class htsjdk.tribble.index.AbstractIndex
 
hasFilterLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
 
hasForbiddenKey(Map<String, Object>) - Static method in class htsjdk.variant.variantcontext.Genotype

Does the attribute map have a mapping involving a forbidden key (i.e.,
 one that's managed inline by this Genotypes object?

hasFormatLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
 
hasGenotype(String) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasGenotypes(Collection<String>) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasGenotypingData() - Method in class htsjdk.variant.vcf.VCFHeader

do we have genotyping data?

hasGQ() - Method in class htsjdk.variant.variantcontext.Genotype

Does the GQ field have a value?

hashCode() - Method in class htsjdk.samtools.Bin

Compute a unique hash code for the given reference sequence and bin number.

hashCode() - Method in class htsjdk.samtools.BinningIndexContent.BinList
 
hashCode() - Method in class htsjdk.samtools.BinningIndexContent
 
hashCode() - Method in class htsjdk.samtools.Chunk
 
hashCode() - Method in class htsjdk.samtools.Cigar
 
hashCode() - Method in class htsjdk.samtools.CigarElement
 
hashCode() - Method in class htsjdk.samtools.cram.common.MutableInt
 
hashCode() - Method in class htsjdk.samtools.cram.structure.ReadTag
 
hashCode() - Method in class htsjdk.samtools.fastq.FastqRecord
 
hashCode() - Method in class htsjdk.samtools.LinearIndex
 
hashCode() - Method in class htsjdk.samtools.metrics.MetricBase

Computes a hashcode by formatting each field into its on disk representation 
 and summing the hashcodes of all the fields.

hashCode() - Method in class htsjdk.samtools.metrics.MetricsFile
 
hashCode() - Method in class htsjdk.samtools.metrics.StringHeader
 
hashCode() - Method in class htsjdk.samtools.metrics.VersionHeader
 
hashCode() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
 
hashCode() - Method in class htsjdk.samtools.SAMFileHeader
 
hashCode() - Method in class htsjdk.samtools.SAMProgramRecord
 
hashCode() - Method in class htsjdk.samtools.SAMReadGroupRecord
 
hashCode() - Method in class htsjdk.samtools.SAMRecord
 
hashCode() - Method in class htsjdk.samtools.SAMSequenceDictionary
 
hashCode() - Method in class htsjdk.samtools.SAMSequenceRecord
 
hashCode() - Method in class htsjdk.samtools.sra.SRALazyRecord

The same approach as with 'equals' method.

hashCode() - Method in class htsjdk.samtools.util.Histogram.Bin
 
hashCode() - Method in class htsjdk.samtools.util.Histogram
 
hashCode() - Method in class htsjdk.samtools.util.Interval
 
hashCode() - Method in class htsjdk.samtools.util.IntervalList
 
hashCode() - Method in class htsjdk.samtools.util.IntervalTreeMap
 
hashCode() - Method in class htsjdk.samtools.util.RelativeIso8601Date
 
hashCode() - Method in class htsjdk.samtools.util.Tuple
 
hashCode() - Method in class htsjdk.tribble.index.interval.Interval
 
hashCode() - Method in class htsjdk.tribble.index.tabix.TabixFormat
 
hashCode() - Method in class htsjdk.tribble.index.tabix.TabixIndex
 
hashCode() - Method in class htsjdk.variant.variantcontext.Allele
 
hashCode() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
hashCode() - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
 
hashCode() - Method in class htsjdk.variant.vcf.VCFHeaderLine
 
hashCode() - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
 
hashUnencodedChars(CharSequence) - Method in class htsjdk.samtools.util.Murmur3

Hashes a character stream to an int using Murmur3.

hasID() - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasIndex() - Method in class htsjdk.samtools.CRAMFileReader
 
hasIndex() - Method in interface htsjdk.samtools.SamReader
 
hasIndex() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
hasIndex() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
hasIndex() - Method in class htsjdk.samtools.SRAFileReader
 
hasIndex() - Method in class htsjdk.tribble.AbstractFeatureReader

Whether the reader has an index or not
 Default implementation returns false

hasIndex() - Method in class htsjdk.tribble.TabixFeatureReader
 
hasIndex() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
 
hasIndexEntry(String) - Method in class htsjdk.samtools.reference.FastaSequenceIndex

Does the given contig name have a corresponding entry?

hasInfoLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
 
hasLikelihoods() - Method in class htsjdk.variant.variantcontext.Genotype
 
hasLog10PError() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
hasLog10PError() - Method in class htsjdk.variant.variantcontext.Genotype

Deprecated.

hasLog10PError() - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasMateCigar(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Checks to see if it is valid for this record to have a mate CIGAR (MC) and then if there is a mate CIGAR available.

hasMD5() - Method in class htsjdk.tribble.index.AbstractIndex
 
hasMergedSequenceDictionary() - Method in class htsjdk.samtools.SamFileHeaderMerger
 
hasNext() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
 
hasNext() - Method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
 
hasNext() - Method in class htsjdk.samtools.CRAMIterator
 
hasNext() - Method in class htsjdk.samtools.DuplicateSetIterator
 
hasNext() - Method in class htsjdk.samtools.fastq.FastqReader
 
hasNext() - Method in class htsjdk.samtools.filter.FilteringSamIterator

Returns true if the iteration has more elements.

hasNext() - Method in class htsjdk.samtools.MergingSamRecordIterator

Returns true if any of the underlying iterators has more records, otherwise false.

hasNext() - Method in class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
 
hasNext() - Method in class htsjdk.samtools.SamReader.AssertingIterator
 
hasNext() - Method in class htsjdk.samtools.sra.SRAAlignmentIterator
 
hasNext() - Method in class htsjdk.samtools.sra.SRAUnalignmentIterator
 
hasNext() - Method in class htsjdk.samtools.SRAIterator

NGS iterators implement a single method "nextObject" which return true if the operation was successful or
 false if there are no more objects available.

hasNext() - Method in class htsjdk.samtools.util.AbstractIterator
 
hasNext() - Method in class htsjdk.samtools.util.AbstractLocusIterator

Returns true if there are more AbstractLocusInfo objects that can be returned, due to any of the following reasons:
 1) there are more aligned reads in the SAM file
 2) there are AbstractLocusInfos in some stage of accumulation
 3) there are loci in the target mask that have yet to be accumulated (even if there are no reads covering them)

hasNext() - Method in class htsjdk.samtools.util.AsyncBufferedIterator
 
hasNext() - Method in class htsjdk.samtools.util.DelegatingIterator
 
hasNext() - Method in class htsjdk.samtools.util.IntervalTree.FwdIterator
 
hasNext() - Method in class htsjdk.samtools.util.IntervalTree.OverlapIterator
 
hasNext() - Method in class htsjdk.samtools.util.IntervalTree.RevIterator
 
hasNext() - Method in class htsjdk.samtools.util.IntervalTree.ValuesIterator
 
hasNext() - Method in class htsjdk.samtools.util.MergingIterator
 
hasNext() - Method in class htsjdk.samtools.util.PeekableIterator

True if there are more items, in which case both next() and peek() will return a value.

hasNext() - Method in class htsjdk.samtools.util.PeekIterator
 
hasNext() - Method in class htsjdk.samtools.util.SortingLongCollection

Call only after doneAddingStartIteration() has been called.

hasNext() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
 
hasNext() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator

Returns true if the iteration has more elements.

hasOriginalMappingInformation(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

See if any tags pertaining to original mapping information have been set.

hasPL() - Method in class htsjdk.variant.variantcontext.Genotype

Does the PL field have a value?

hasProgramGroupCollisions() - Method in class htsjdk.samtools.SamFileHeaderMerger

Returns true if there are program group duplicates within the merged headers.

hasReadGroupCollisions() - Method in class htsjdk.samtools.SamFileHeaderMerger

Returns true if there are read group duplicates within the merged headers.

hasSameAllelesAs(VariantContext) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasSameAlternateAllelesAs(VariantContext) - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasSymbolicAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext
 
hasSymbolicAlleles(List<Allele>) - Static method in class htsjdk.variant.variantcontext.VariantContext
 
hasTimestamp() - Method in class htsjdk.tribble.index.AbstractIndex
 
hasValueDeterminedNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
hasValueDeterminedNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
 
header - Variable in class htsjdk.samtools.cram.structure.Container
 
Header - Interface in htsjdk.samtools.metrics

A header for a metrics file.

header - Variable in class htsjdk.tribble.AbstractFeatureReader
 
header - Variable in class htsjdk.variant.bcf2.BCF2Codec.LazyData
 
header - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
HEADER_INDICATOR - Static variable in class htsjdk.variant.vcf.VCFHeader
 
HEADER_LINE - Static variable in class htsjdk.tribble.example.ExampleBinaryCodec
 
headerBlock - Variable in class htsjdk.samtools.cram.structure.Slice
 
headerLinesAreOrderedConsistently(VCFHeader, VCFHeader) - Static method in class htsjdk.variant.bcf2.BCF2Utils

Are the elements and their order in the output and input headers consistent so that
 we can write out the raw genotypes block without decoding and recoding it?

 If the order of INFO, FILTER, or contrig elements in the output header is different than
 in the input header we must decode the blocks using the input header and then recode them
 based on the new output order.

headRecordIsFromDisk() - Method in class htsjdk.samtools.util.DiskBackedQueue
 
HeterozygosityFilter - Class in htsjdk.variant.variantcontext.filter

A Predicate on VariantContexts that either returns true at heterozygous sites (invertible to false).

HeterozygosityFilter(boolean, String) - Constructor for class htsjdk.variant.variantcontext.filter.HeterozygosityFilter

Constructor for a filter that will keep (or remove, if keepHets is false) VC for which the
 genotype of sample is heterozygous.

HeterozygosityFilter(boolean) - Constructor for class htsjdk.variant.variantcontext.filter.HeterozygosityFilter

Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.

hexStringToBytes(String) - Static method in class htsjdk.samtools.util.StringUtil

Convert a String containing hex characters into an array of bytes with the binary representation
 of the hex string

HI - Variable in class htsjdk.samtools.SAMTagUtil
 
HIGH_ACCURACY_DESCRIPTION - Static variable in class htsjdk.samtools.DownsamplingIteratorFactory
 
higher_than_mapping_score(int) - Static method in class htsjdk.samtools.cram.lossy.ReadCategory
 
HISTO_HEADER - Static variable in class htsjdk.samtools.metrics.MetricsFile
 
Histogram<K extends java.lang.Comparable> - Class in htsjdk.samtools.util

Class for computing and accessing histogram type data.

Histogram() - Constructor for class htsjdk.samtools.util.Histogram

Constructs a new Histogram with default bin and value labels.

Histogram(String, String) - Constructor for class htsjdk.samtools.util.Histogram

Constructs a new Histogram with supplied bin and value labels.

Histogram(Comparator<? super K>) - Constructor for class htsjdk.samtools.util.Histogram

Constructs a new Histogram that'll use the supplied comparator to sort keys.

Histogram(String, String, Comparator<? super K>) - Constructor for class htsjdk.samtools.util.Histogram

Constructor that takes labels for the bin and values and a comparator to sort the bins.

Histogram(Histogram<K>) - Constructor for class htsjdk.samtools.util.Histogram

Copy constructor for a histogram.

Histogram.Bin<K extends java.lang.Comparable> - Class in htsjdk.samtools.util

Represents a bin in the Histogram.

htsjdk.samtools - package htsjdk.samtools
 
htsjdk.samtools.apps - package htsjdk.samtools.apps
 
htsjdk.samtools.cram - package htsjdk.samtools.cram
 
htsjdk.samtools.cram.build - package htsjdk.samtools.cram.build
 
htsjdk.samtools.cram.common - package htsjdk.samtools.cram.common
 
htsjdk.samtools.cram.digest - package htsjdk.samtools.cram.digest
 
htsjdk.samtools.cram.encoding - package htsjdk.samtools.cram.encoding
 
htsjdk.samtools.cram.encoding.huffman - package htsjdk.samtools.cram.encoding.huffman
 
htsjdk.samtools.cram.encoding.huffman.codec - package htsjdk.samtools.cram.encoding.huffman.codec
 
htsjdk.samtools.cram.encoding.rans - package htsjdk.samtools.cram.encoding.rans
 
htsjdk.samtools.cram.encoding.reader - package htsjdk.samtools.cram.encoding.reader
 
htsjdk.samtools.cram.encoding.readfeatures - package htsjdk.samtools.cram.encoding.readfeatures
 
htsjdk.samtools.cram.encoding.writer - package htsjdk.samtools.cram.encoding.writer
 
htsjdk.samtools.cram.io - package htsjdk.samtools.cram.io
 
htsjdk.samtools.cram.lossy - package htsjdk.samtools.cram.lossy
 
htsjdk.samtools.cram.ref - package htsjdk.samtools.cram.ref
 
htsjdk.samtools.cram.structure - package htsjdk.samtools.cram.structure
 
htsjdk.samtools.example - package htsjdk.samtools.example
 
htsjdk.samtools.fastq - package htsjdk.samtools.fastq
 
htsjdk.samtools.filter - package htsjdk.samtools.filter
 
htsjdk.samtools.liftover - package htsjdk.samtools.liftover
 
htsjdk.samtools.metrics - package htsjdk.samtools.metrics
 
htsjdk.samtools.reference - package htsjdk.samtools.reference
 
htsjdk.samtools.seekablestream - package htsjdk.samtools.seekablestream
 
htsjdk.samtools.sra - package htsjdk.samtools.sra
 
htsjdk.samtools.util - package htsjdk.samtools.util
 
htsjdk.samtools.util.ftp - package htsjdk.samtools.util.ftp
 
htsjdk.samtools.util.zip - package htsjdk.samtools.util.zip
 
htsjdk.tribble - package htsjdk.tribble
 
htsjdk.tribble.annotation - package htsjdk.tribble.annotation
 
htsjdk.tribble.bed - package htsjdk.tribble.bed
 
htsjdk.tribble.example - package htsjdk.tribble.example
 
htsjdk.tribble.exception - package htsjdk.tribble.exception
 
htsjdk.tribble.gelitext - package htsjdk.tribble.gelitext
 
htsjdk.tribble.index - package htsjdk.tribble.index
 
htsjdk.tribble.index.interval - package htsjdk.tribble.index.interval
 
htsjdk.tribble.index.linear - package htsjdk.tribble.index.linear
 
htsjdk.tribble.index.tabix - package htsjdk.tribble.index.tabix
 
htsjdk.tribble.readers - package htsjdk.tribble.readers
 
htsjdk.tribble.util - package htsjdk.tribble.util
 
htsjdk.tribble.util.popgen - package htsjdk.tribble.util.popgen
 
htsjdk.variant.bcf2 - package htsjdk.variant.bcf2
 
htsjdk.variant.example - package htsjdk.variant.example
 
htsjdk.variant.utils - package htsjdk.variant.utils
 
htsjdk.variant.variantcontext - package htsjdk.variant.variantcontext
 
htsjdk.variant.variantcontext.filter - package htsjdk.variant.variantcontext.filter
 
htsjdk.variant.variantcontext.writer - package htsjdk.variant.variantcontext.writer
 
htsjdk.variant.vcf - package htsjdk.variant.vcf
 
HTTPHelper - Class in htsjdk.tribble.util

Simple implementation of URLHelper based on the JDK URL and HttpURLConnection classes.

HTTPHelper(URL) - Constructor for class htsjdk.tribble.util.HTTPHelper
 
HttpUtils - Class in htsjdk.samtools.util

User: jrobinso
 Date: Sep 23, 2009

HttpUtils() - Constructor for class htsjdk.samtools.util.HttpUtils
 
HuffmanByteEncoding - Class in htsjdk.samtools.cram.encoding.huffman.codec
 
HuffmanByteEncoding() - Constructor for class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanByteEncoding
 
HuffmanCode - Class in htsjdk.samtools.cram.encoding.huffman
 
HuffmanCode() - Constructor for class htsjdk.samtools.cram.encoding.huffman.HuffmanCode
 
HuffmanIntegerEncoding - Class in htsjdk.samtools.cram.encoding.huffman.codec
 
HuffmanIntegerEncoding() - Constructor for class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding
 
HuffmanTree<T> - Class in htsjdk.samtools.cram.encoding.huffman
 
hwCalculate(int, int, int) - Static method in class htsjdk.tribble.util.popgen.HardyWeinbergCalculation

Calculates exact two-sided hardy-weinberg p-value.





I

id() - Method in class htsjdk.samtools.cram.encoding.BetaIntegerEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding
 
id() - Method in interface htsjdk.samtools.cram.encoding.Encoding
 
id() - Method in class htsjdk.samtools.cram.encoding.ExternalByteArrayEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.ExternalByteEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.ExternalIntegerEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.ExternalLongEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.GammaIntegerEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.GolombIntegerEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.GolombLongEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.GolombRiceIntegerEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanByteEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.NullEncoding
 
id() - Method in class htsjdk.samtools.cram.encoding.SubexponentialIntegerEncoding
 
id - Variable in class htsjdk.samtools.cram.structure.EncodingParams
 
id(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells us that the resulting VariantContext should have ID

ID_FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
ID_TO_ENUM - Static variable in class htsjdk.variant.bcf2.BCF2Utils
 
IGFGenotypesWriter(VCFHeader, BCF2FieldEncoder, IntGenotypeFieldAccessors.Accessor) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
 
ignorePositionsWithQualityScore - Static variable in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
ignoreTags - Variable in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
IH - Variable in class htsjdk.samtools.SAMTagUtil
 
ILLUMINA_TO_PHRED_SUBTRAHEND - Static variable in class htsjdk.samtools.util.SolexaQualityConverter

This value is removed from an Illumina 1.8 quality score to make it a Phred score

immutable() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
includeIndels - Variable in class htsjdk.samtools.util.AbstractLocusIterator

If true, include indels in the LocusInfo

INCORRECT_HEADER_SIZE_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
 
increment(K) - Method in class htsjdk.samtools.util.Histogram

Increments the value in the designated bin by 1.

increment(K, double) - Method in class htsjdk.samtools.util.Histogram

Increments the value in the designated bin by the supplied increment.

incrementFeatureCount() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
index - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
index - Variable in class htsjdk.samtools.cram.structure.Slice
 
index(File) - Method in class htsjdk.samtools.SamInputResource

Updates the index to point at the provided resource, then returns itself.

index(Path) - Method in class htsjdk.samtools.SamInputResource

Updates the index to point at the provided resource, then returns itself.

index(InputStream) - Method in class htsjdk.samtools.SamInputResource

Updates the index to point at the provided resource, then returns itself.

index(URL) - Method in class htsjdk.samtools.SamInputResource

Updates the index to point at the provided resource, then returns itself.

index(SeekableStream) - Method in class htsjdk.samtools.SamInputResource

Updates the index to point at the provided resource, then returns itself.

Index - Interface in htsjdk.tribble.index

Interface for all index implementations.

INDEX_TYPE - Static variable in class htsjdk.tribble.index.interval.IntervalTreeIndex
 
INDEX_TYPE - Static variable in class htsjdk.tribble.index.linear.LinearIndex
 
IndexCreator - Interface in htsjdk.tribble.index

An interface for creating indexes

IndexedFastaSequenceFile - Class in htsjdk.samtools.reference

A fasta file driven by an index for fast, concurrent lookups.

IndexedFastaSequenceFile(File, FastaSequenceIndex) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile

Open the given indexed fasta sequence file.

IndexedFastaSequenceFile(File) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile

Open the given indexed fasta sequence file.

IndexedFastaSequenceFile(Path, FastaSequenceIndex) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile

Open the given indexed fasta sequence file.

IndexedFastaSequenceFile(Path) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile

Open the given indexed fasta sequence file.

indexedFile - Variable in class htsjdk.tribble.index.AbstractIndex
 
indexedFileMD5 - Variable in class htsjdk.tribble.index.AbstractIndex
 
indexedFileSize - Variable in class htsjdk.tribble.index.AbstractIndex
 
indexedFileTS - Variable in class htsjdk.tribble.index.AbstractIndex
 
IndexFactory - Class in htsjdk.tribble.index

Factory class for creating indexes.

IndexFactory() - Constructor for class htsjdk.tribble.index.IndexFactory
 
IndexFactory.IndexBalanceApproach - Enum in htsjdk.tribble.index

We can optimize index-file-creation for different factors.

IndexFactory.IndexType - Enum in htsjdk.tribble.index

an enum that contains all of the information about the index types, and how to create them

indexFile(String) - Static method in class htsjdk.tribble.Tribble

Return the name of the index file for the provided vcf filename
 Does not actually create an index

indexFile(File) - Static method in class htsjdk.tribble.Tribble

Return the File of the index file for the provided vcf file
 Does not actually create an index

indexing() - Method in interface htsjdk.samtools.SamReader

Exposes the SamReader.Indexing facet of this SamReader.

indexing() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
indexOf(Object) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
IndexToTable - Class in htsjdk.tribble.example
 
IndexToTable() - Constructor for class htsjdk.tribble.example.IndexToTable
 
IndicesAreEqual - Class in htsjdk.tribble.example

Check with two index files are equal

IndicesAreEqual() - Constructor for class htsjdk.tribble.example.IndicesAreEqual
 
info(Throwable, Object...) - Method in class htsjdk.samtools.util.Log

Logs a Throwable and optional message parts at level info.

info(Object...) - Method in class htsjdk.samtools.util.Log

Logs one or more message parts at level info.

INFO_FIELD_ARRAY_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
INFO_FIELD_ARRAY_SEPARATOR_CHAR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
INFO_FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
INFO_FIELD_SEPARATOR_CHAR - Static variable in class htsjdk.variant.vcf.VCFConstants
 
INFO_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
 
initialize(String, Map<String, String>) - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
 
initializeAnyploidPLIndexToAlleleIndices(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

Initialize cache of allele anyploid indices
 If initialized multiple times with the same ploidy, the alternate alleles from the last initialization will be used

initializeCigar(Cigar) - Method in class htsjdk.samtools.SAMRecord

For setting the Cigar string when BAMRecord has decoded it.

initializeMatchExps(String[], String[]) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Method for creating JexlVCMatchExp from input walker arguments names and exps.

initializeMatchExps(List<String>, List<String>) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Method for creating JexlVCMatchExp from input walker arguments names and exps.

initializeMatchExps(Map<String, String>) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Method for creating JexlVCMatchExp from input walker arguments mapping from names to exps.

InputStreamUtils - Class in htsjdk.samtools.cram.io

Convenience methods to read from InputStream.

InputStreamUtils() - Constructor for class htsjdk.samtools.cram.io.InputStreamUtils
 
insert(SAMBinaryTagAndValue) - Method in class htsjdk.samtools.SAMBinaryTagAndValue

Inserts at item into the ordered list of attributes and returns the head of the list/sub-list

insert(Interval) - Method in class htsjdk.tribble.index.interval.IntervalTree
 
insert(Interval) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
 
insert(String, Interval) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex

Add a new interval to this index

InsertBase - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing a single insert base.

InsertBase() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
InsertBase(int, byte) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
INSERTION - Static variable in enum htsjdk.samtools.CigarOperator
 
Insertion - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing a multi-base insertion.

Insertion() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
Insertion(int, byte[]) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
insertion() - Static method in class htsjdk.samtools.cram.lossy.BaseCategory
 
INSERTION_ALLELE_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
insertionCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
insertionCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
insertSizeCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
InsertSizeFilter - Class in htsjdk.samtools.filter

Filter things that fall outside a specified range of insert sizes.

InsertSizeFilter(int, int) - Constructor for class htsjdk.samtools.filter.InsertSizeFilter
 
int32(InputStream) - Static method in class htsjdk.samtools.cram.io.CramInt

Read unsigned little-endian 4 byte integer from an InputStream.

int32(byte[]) - Static method in class htsjdk.samtools.cram.io.CramInt

Read unsigned little-endian 4 byte integer from an array of bytes.

int32(ByteBuffer) - Static method in class htsjdk.samtools.cram.io.CramInt

Read unsigned little-endian 4 byte integer from an ByteBuffer.

IntArray(VCFCompoundHeaderLine, Map<String, Integer>) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
 
INTEGER_TYPES_BY_SIZE - Static variable in class htsjdk.variant.bcf2.BCF2Utils
 
IntegerTypeGenotypesWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IntegerTypeGenotypesWriter
 
InternalCodecException(String) - Constructor for exception htsjdk.tribble.TribbleException.InternalCodecException
 
intersect(CRAIEntry, CRAIEntry) - Static method in class htsjdk.samtools.cram.CRAIEntry
 
intersect(Interval) - Method in class htsjdk.samtools.util.Interval

Returns a new Interval that represents the intersection between the two intervals.

intersection(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList

A utility function for generating the intersection of two IntervalLists, checks for equal dictionaries.

intersection(Collection<IntervalList>) - Static method in class htsjdk.samtools.util.IntervalList

A utility function for intersecting a list of IntervalLists, checks for equal dictionaries.

intersects(Interval) - Method in class htsjdk.samtools.util.Interval

Returns true if this interval overlaps the other interval, otherwise false.

Interval - Class in htsjdk.samtools.util

Represents a simple interval on a sequence.

Interval(String, int, int) - Constructor for class htsjdk.samtools.util.Interval

Constructs an interval with the supplied sequence and start and end.

Interval(String, int, int, boolean, String) - Constructor for class htsjdk.samtools.util.Interval

Constructs an interval with the supplied sequence and start, end, strand and name.

Interval - Class in htsjdk.tribble.index.interval

Quick and dirty interval class
  Describes a genomic interval and where in a file information for that
  interval can be obtained

Interval(int, int) - Constructor for class htsjdk.tribble.index.interval.Interval
 
Interval(int, int, Block) - Constructor for class htsjdk.tribble.index.interval.Interval
 
INTERVAL_LIST_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IntervalList
 
INTERVAL_LIST_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
 
INTERVAL_MERGING_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
 
INTERVAL_PADDING_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
 
INTERVAL_SET_RULE_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
 
IntervalFilter - Class in htsjdk.samtools.filter

Filter SAMRecords so that only those that overlap the given list of intervals.

IntervalFilter(List<Interval>, SAMFileHeader) - Constructor for class htsjdk.samtools.filter.IntervalFilter

Prepare to filter out SAMRecords that do not overlap the given list of intervals

IntervalIndexCreator - Class in htsjdk.tribble.index.interval

Creates interval indexes from a stream of features

IntervalIndexCreator(File, int) - Constructor for class htsjdk.tribble.index.interval.IntervalIndexCreator
 
IntervalIndexCreator(File) - Constructor for class htsjdk.tribble.index.interval.IntervalIndexCreator
 
IntervalKeepPairFilter - Class in htsjdk.samtools.filter

Filter out SAMRecords where neither record of a pair overlaps a given set of
 intervals.

IntervalKeepPairFilter(List<Interval>) - Constructor for class htsjdk.samtools.filter.IntervalKeepPairFilter

Prepare to filter out SAMRecords that do not overlap the given list of
 intervals

IntervalList - Class in htsjdk.samtools.util

Represents a list of intervals against a reference sequence that can be written to
 and read from a file.

IntervalList(SAMFileHeader) - Constructor for class htsjdk.samtools.util.IntervalList

Constructs a new interval list using the supplied header information.

IntervalList(SAMSequenceDictionary) - Constructor for class htsjdk.samtools.util.IntervalList

Constructs a new interval list using the supplied header information.

IntervalListReferenceSequenceMask - Class in htsjdk.samtools.util

Serve up loci of interest based on an interval list.

IntervalListReferenceSequenceMask(IntervalList) - Constructor for class htsjdk.samtools.util.IntervalListReferenceSequenceMask
 
INTERVALS_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
 
IntervalTree<V> - Class in htsjdk.samtools.util

A Red-Black tree with intervals for keys.

IntervalTree() - Constructor for class htsjdk.samtools.util.IntervalTree
 
IntervalTree - Class in htsjdk.tribble.index.interval

An implementation of an interval tree, following the explanation.

IntervalTree() - Constructor for class htsjdk.tribble.index.interval.IntervalTree
 
IntervalTree.FwdIterator - Class in htsjdk.samtools.util
 
IntervalTree.Node<V1> - Class in htsjdk.samtools.util
 
IntervalTree.OverlapIterator - Class in htsjdk.samtools.util
 
IntervalTree.RevIterator - Class in htsjdk.samtools.util
 
IntervalTree.ValuesIterator<V1> - Class in htsjdk.samtools.util
 
IntervalTreeIndex - Class in htsjdk.tribble.index.interval

Index based on an interval tree

IntervalTreeIndex(InputStream) - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex

Load from file.

IntervalTreeIndex(String) - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex

Prepare to build an index.

IntervalTreeIndex.ChrIndex - Class in htsjdk.tribble.index.interval
 
IntervalTreeMap<T> - Class in htsjdk.samtools.util

Utility class that implements an interval map.

IntervalTreeMap() - Constructor for class htsjdk.samtools.util.IntervalTreeMap
 
IntervalTreeMap(Map<? extends Interval, ? extends T>) - Constructor for class htsjdk.samtools.util.IntervalTreeMap
 
IntervalUtil - Class in htsjdk.samtools.util
 
IntervalUtil() - Constructor for class htsjdk.samtools.util.IntervalUtil
 
IntGenotypeFieldAccessors - Class in htsjdk.variant.variantcontext.writer

A convenient way to provide a single view on the many int and int[] field values we work with,
 for writing out the values.

IntGenotypeFieldAccessors() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors
 
IntGenotypeFieldAccessors.Accessor - Class in htsjdk.variant.variantcontext.writer
 
IntGenotypeFieldAccessors.ADAccessor - Class in htsjdk.variant.variantcontext.writer
 
IntGenotypeFieldAccessors.DPAccessor - Class in htsjdk.variant.variantcontext.writer
 
IntGenotypeFieldAccessors.GQAccessor - Class in htsjdk.variant.variantcontext.writer
 
IntGenotypeFieldAccessors.PLAccessor - Class in htsjdk.variant.variantcontext.writer
 
IntHashMap<T> - Class in htsjdk.samtools.cram.common


 A hash map that uses primitive ints for the key rather than objects.

IntHashMap() - Constructor for class htsjdk.samtools.cram.common.IntHashMap


 Constructs a new, empty hashtable with a default capacity and load
 factor, which is 20 and 0.75 respectively.

IntHashMap(int) - Constructor for class htsjdk.samtools.cram.common.IntHashMap


 Constructs a new, empty hashtable with the specified initial capacity and
 default load factor, which is 0.75.

IntHashMap(int, float) - Constructor for class htsjdk.samtools.cram.common.IntHashMap


 Constructs a new, empty hashtable with the specified initial capacity and
 the specified load factor.

intToNameType3Bytes(int) - Static method in class htsjdk.samtools.cram.structure.ReadTag
 
intToNameType4Bytes(int) - Static method in class htsjdk.samtools.cram.structure.ReadTag
 
intValue() - Method in enum htsjdk.samtools.SAMFlag
 
intValuesToString(int[]) - Static method in class htsjdk.samtools.util.StringUtil
 
intValuesToString(short[]) - Static method in class htsjdk.samtools.util.StringUtil
 
INVALID_FILE_PTR_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
 
invalidateSampleNameMap() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
invalidateSampleNameMap() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
 
invalidateSampleOrdering() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
invalidateSampleOrdering() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
 
InvalidDateException() - Constructor for exception htsjdk.samtools.util.DateParser.InvalidDateException
 
InvalidDateException(String) - Constructor for exception htsjdk.samtools.util.DateParser.InvalidDateException
 
InvalidDateException(String, Throwable) - Constructor for exception htsjdk.samtools.util.DateParser.InvalidDateException
 
InvalidDateException(Throwable) - Constructor for exception htsjdk.samtools.util.DateParser.InvalidDateException
 
InvalidDecodeLine(String, String) - Constructor for exception htsjdk.tribble.TribbleException.InvalidDecodeLine
 
InvalidDecodeLine(String, int) - Constructor for exception htsjdk.tribble.TribbleException.InvalidDecodeLine
 
InvalidHeader(String) - Constructor for exception htsjdk.tribble.TribbleException.InvalidHeader
 
invert(IntervalList) - Static method in class htsjdk.samtools.util.IntervalList

inverts an IntervalList and returns one that has exactly all the bases in the dictionary that the original one does not.

IOUtil - Class in htsjdk.samtools.util

Miscellaneous stateless static IO-oriented methods.

IOUtil() - Constructor for class htsjdk.samtools.util.IOUtil
 
IS_ADJACENT_AND_EMPTY - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
IS_LEFT_OVERHANGING_OVERLAPPER - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
IS_RIGHT_OVERHANGING_OVERLAPPER - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
IS_STRICTLY_GREATER - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
IS_STRICTLY_LESS - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
IS_SUBSET - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
IS_SUPERSET - Static variable in class htsjdk.samtools.util.IntervalTree.Node
 
isAdjacent(IntervalTree.Node<V1>) - Method in class htsjdk.samtools.util.IntervalTree.Node
 
isAdjacentTo(Chunk) - Method in class htsjdk.samtools.Chunk

Returns whether two chunks overlap.

isAlignment() - Method in enum htsjdk.samtools.CigarOperator

Returns true if the operator is a M, a X or a EQ

isAllowedAttributeValue(Object) - Static method in class htsjdk.samtools.SAMBinaryTagAndValue
 
isAllowedAttributeValue(Object) - Static method in class htsjdk.samtools.SAMRecord

Deprecated.
The attribute type and value checks have been moved directly into
 SAMBinaryTagAndValue.


isAtLeastAsRecentAs(VCFHeaderVersion) - Method in enum htsjdk.variant.vcf.VCFHeaderVersion

Determines whether this version is at least as recent as a given version

isAvailable() - Method in class htsjdk.variant.variantcontext.Genotype
 
isBamFile(File) - Static method in class htsjdk.samtools.BamFileIoUtils
 
isBAMFile(InputStream) - Static method in class htsjdk.samtools.SamStreams
 
isBCF(File) - Static method in class htsjdk.variant.vcf.VCFFileReader

Returns true if the given file appears to be a BCF file.

isBCFOutput(File) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.
Should we output a BCF file based solely on the name of the file at location?

isBCFOutput(File, EnumSet<Options>) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.
 
isBiallelic() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isBisulfiteConverted(byte, byte, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil

Checks for bisulfite conversion, C->T on the positive strand and G->A on the negative strand.

isBisulfiteConverted(byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil
 
isBisulfiteSequenced() - Method in class htsjdk.samtools.SamFileValidator
 
isBlank(String) - Static method in class htsjdk.samtools.util.StringUtil

Checks if a String is whitespace, empty ("") or null.

isCalled() - Method in class htsjdk.variant.variantcontext.Allele
 
isCalled() - Method in class htsjdk.variant.variantcontext.Genotype
 
isCaptureAllTags() - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
isCaptureAllTags() - Method in class htsjdk.samtools.CRAMFileWriter
 
isCaptureReadNames() - Method in class htsjdk.samtools.cram.encoding.writer.Writer
 
isClipped() - Method in class htsjdk.samtools.Cigar

returns true if the cigar is clipped

isClipping() - Method in enum htsjdk.samtools.CigarOperator

Returns true if the operator is a clipped (hard or soft) operator

isCollapsedString(String) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
isCompatible(Collection<VCFContigHeaderLine>) - Method in class htsjdk.variant.variantcontext.VariantContextComparator

Returns true if the given header lines are from a file sorted according to this VariantContextComparator.

isComplexIndel() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isCompressedVcf(File) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.
 
isCRAMFile(InputStream) - Static method in class htsjdk.samtools.SamStreams
 
isCurrentVersion() - Method in class htsjdk.tribble.index.AbstractIndex

check the current version against the version we read in

isCurrentVersion() - Method in interface htsjdk.tribble.index.Index
 
isCurrentVersion() - Method in class htsjdk.tribble.index.linear.LinearIndex
 
isCurrentVersion() - Method in class htsjdk.tribble.index.tabix.TabixIndex
 
isDestructiveIteration() - Method in class htsjdk.samtools.util.SortingCollection
 
isDetached() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isDeterminationAmbiguous() - Method in class htsjdk.samtools.util.QualityEncodingDetector

Tests whether or not the detector can make a determination without guessing (i.e., if all but one quality format
 can be excluded using established exclusion conventions).

isDone(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec
 
isDone(PositionalBufferedStream) - Method in class htsjdk.tribble.BinaryFeatureCodec
 
isDone(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec

Adapter method that assesses whether the provided SOURCE has more data.

isDone() - Method in interface htsjdk.tribble.readers.Positional

Is the stream done?  Equivalent to ! hasNext() for an iterator?

isDone() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
 
isDuplicate() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isDynamicallyTyped() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

Is the BCF2 type of this field static, or does it have to be determine from
 the actual field value itself?

ISeekableStreamFactory - Interface in htsjdk.samtools.seekablestream

Factory for creating SeekableStreams based on URLs/paths.

isEmitUncoveredLoci() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
isEmpty() - Method in class htsjdk.samtools.BAMFileSpan

Does this chunk list map to any position within the BAM file?

isEmpty() - Method in class htsjdk.samtools.Cigar
 
isEmpty() - Method in class htsjdk.samtools.cram.common.IntHashMap


 Tests if this hashtable maps no keys to values.

isEmpty() - Method in class htsjdk.samtools.DuplicateSet
 
isEmpty() - Method in interface htsjdk.samtools.SAMFileSpan

Does this file span point to any data, or is it completely empty?

isEmpty() - Method in class htsjdk.samtools.SAMSequenceDictionary
 
isEmpty() - Method in class htsjdk.samtools.util.AbstractLocusInfo
 
isEmpty() - Method in class htsjdk.samtools.util.DiskBackedQueue
 
isEmpty() - Method in class htsjdk.samtools.util.Histogram

Returns true if this histogram has no data in in, false otherwise.

isEmpty() - Method in class htsjdk.samtools.util.IntervalTreeMap
 
isEmpty() - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
 
isEmpty() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer

Returns true if we are tracking no records, false otherwise

isEmpty() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
isEmpty() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
 
isEnabled(Log.LogLevel) - Static method in class htsjdk.samtools.util.Log

Returns true if the specified log level is enabled otherwise false.

isEOF() - Method in class htsjdk.samtools.cram.structure.Container
 
isFilePath(String) - Static method in class htsjdk.samtools.seekablestream.SeekableStreamFactory

Does this path point to a regular file on disk and not something like a URL?

isFiltered() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
isFiltered() - Method in class htsjdk.variant.variantcontext.Genotype

Is this genotype filtered or not?

isFiltered() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isFirstSegment() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isFixedCount() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
isForbiddenKey(String) - Static method in class htsjdk.variant.variantcontext.Genotype
 
isForcePreserveQualityScores() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isFormatString(String) - Static method in enum htsjdk.variant.vcf.VCFHeaderVersion

are we a valid format string for some type

isFullyDecoded() - Method in class htsjdk.variant.variantcontext.VariantContext

See VariantContext document about fully decoded

isFullyDecoded() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
 
isGzippedSAMFile(InputStream) - Static method in class htsjdk.samtools.SamStreams

Checks whether the file is a gzipped sam file.

isHasMateDownStream() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isHeaderLine(String) - Static method in class htsjdk.variant.vcf.VCFHeaderLine
 
isHet() - Method in enum htsjdk.tribble.gelitext.DiploidGenotype

Deprecated.
 
isHet() - Method in class htsjdk.variant.variantcontext.Genotype
 
isHetNonRef() - Method in class htsjdk.variant.variantcontext.Genotype
 
isHigherAccuracy() - Method in class htsjdk.samtools.DownsamplingIterator

Indicates whether or not the strategy implemented by this DownsamplingIterator makes any effort to
 increase accuracy beyond random sampling (i.e.

isHom() - Method in class htsjdk.variant.variantcontext.Genotype
 
isHomRef() - Method in class htsjdk.variant.variantcontext.Genotype
 
isHomVar() - Method in class htsjdk.variant.variantcontext.Genotype
 
isIncludeIndels() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
isIncludeNonPfReads() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
isIndel() - Method in enum htsjdk.samtools.CigarOperator

Returns true if the operator is a Insertion or Deletion operator

isIndel() - Method in class htsjdk.variant.variantcontext.VariantContext

convenience method for indels

isIndelOrSkippedRegion() - Method in enum htsjdk.samtools.CigarOperator

Returns true if the operator is a Skipped Region Insertion or Deletion operator

isIndexed() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
 
isIndexed() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
 
isIndexed() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
isInitialized() - Method in class htsjdk.samtools.util.Lazy
 
isIntegerType() - Method in enum htsjdk.variant.bcf2.BCF2Type
 
isIterating() - Method in class htsjdk.samtools.util.AbstractIterator
 
isLastSegment() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isLazyWithData() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
isLeftClipped() - Method in class htsjdk.samtools.Cigar

returns true if the cigar string starts With a clipping operator

isMapped() - Method in class htsjdk.samtools.cram.structure.Slice
 
isMateNegativeStrand() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isMateUnmapped() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isMissingType() - Method in enum htsjdk.variant.bcf2.BCF2Type
 
isMixed() - Method in class htsjdk.variant.variantcontext.Genotype
 
isMixed() - Method in class htsjdk.variant.variantcontext.VariantContext

convenience method for indels

isMNP() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isMonomorphicInSamples() - Method in class htsjdk.variant.variantcontext.VariantContext

Genotype-specific functions -- are the genotypes monomorphic w.r.t.

isMultiFragment() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isMultiref() - Method in class htsjdk.samtools.cram.structure.Slice
 
isMutable() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
isNegativeStrand() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isNegativeStrand() - Method in class htsjdk.samtools.util.Interval

Returns true if the interval is on the negative strand, otherwise false.

isNoCall(byte) - Static method in class htsjdk.samtools.util.SequenceUtil

returns true if the value of base represents a no call

isNoCall() - Method in class htsjdk.variant.variantcontext.Allele
 
isNoCall() - Method in class htsjdk.variant.variantcontext.Genotype
 
isNonInformative() - Method in class htsjdk.variant.variantcontext.Genotype

Are all likelihoods for this sample non-informative?

 Returns true if all PLs are 0 => 0,0,0 => true
 0,0,0,0,0,0 => true
 0,10,100 => false

isNonReference() - Method in class htsjdk.variant.variantcontext.Allele
 
isNotFiltered() - Method in class htsjdk.variant.variantcontext.CommonInfo
 
isNotFiltered() - Method in class htsjdk.variant.variantcontext.VariantContext
 
Iso8601Date - Class in htsjdk.samtools.util

Use this type rather than java.util.Date in command-line options in order to get ISO 8601 parsing.

Iso8601Date(String) - Constructor for class htsjdk.samtools.util.Iso8601Date
 
Iso8601Date(Date) - Constructor for class htsjdk.samtools.util.Iso8601Date
 
isPadding() - Method in enum htsjdk.samtools.CigarOperator

Returns true if the operator is a Padding operator

isPhased() - Method in class htsjdk.variant.variantcontext.FastGenotype
 
isPhased() - Method in class htsjdk.variant.variantcontext.Genotype

Are the alleles phased w.r.t.

isPointEvent() - Method in class htsjdk.variant.variantcontext.VariantContext

convenience method for point events

isPolymorphicInSamples() - Method in class htsjdk.variant.variantcontext.VariantContext

Genotype-specific functions -- are the genotypes polymorphic w.r.t.

isPositiveCompletion() - Method in class htsjdk.samtools.util.ftp.FTPReply

Determine if a reply code is a positive completion response.

isPositiveIntermediate() - Method in class htsjdk.samtools.util.ftp.FTPReply

Determine if a reply code is a positive intermediate response.

isPositiveStrand() - Method in class htsjdk.samtools.util.Interval

Returns true if the interval is on the positive strand, otherwise false.

isPreserveReadNames() - Method in class htsjdk.samtools.cram.build.ContainerFactory
 
isPreserveReadNames() - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
isPreserveReadNames() - Method in class htsjdk.samtools.CRAMFileWriter
 
isProperPair() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isProperPair(SAMRecord, SAMRecord, List<SamPairUtil.PairOrientation>) - Static method in class htsjdk.samtools.SamPairUtil
 
isReference() - Method in class htsjdk.variant.variantcontext.Allele
 
isRegularPath(File) - Static method in class htsjdk.samtools.util.IOUtil
 
isRightClipped() - Method in class htsjdk.samtools.Cigar

returns true if the cigar string ends With a clipping operator

isSameSequence(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMSequenceRecord

Looser comparison than equals().

isSecondaryAlignment() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isSecondaryOrSupplementary() - Method in class htsjdk.samtools.SAMRecord

Tests if this record is either a secondary and/or supplementary alignment;
 equivalent to (getNotPrimaryAlignmentFlag() || getSupplementaryAlignmentFlag()).

isSegmentUnmapped() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isSet(int) - Method in enum htsjdk.samtools.SAMFlag
 
isSimpleDeletion() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isSimpleIndel() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isSimpleInsertion() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isSNP() - Method in class htsjdk.variant.variantcontext.VariantContext

convenience method for SNPs

isSorted(SAMRecord) - Method in class htsjdk.samtools.SAMSortOrderChecker

Check if given SAMRecord violates sort order relative to previous SAMRecord.

isSorted(Iterable<T>) - Static method in class htsjdk.tribble.util.ParsingUtils
 
isStaticallyTyped() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

Is the BCF2 type of this field static, or does it have to be determine from
 the actual field value itself?

isStructuralIndel() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isSuccess() - Method in class htsjdk.samtools.util.ftp.FTPReply
 
issueEOF(Version, OutputStream) - Static method in class htsjdk.samtools.cram.build.CramIO

Write an end-of-file marker to the OutputStream.

isSupplementary() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isSupported() - Static method in class htsjdk.samtools.sra.SRAAccession

Deprecated.
use SRAAccession.checkIfInitialized() instead


isSymbolic() - Method in class htsjdk.variant.variantcontext.Allele
 
isSymbolic() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isSymbolicOrSV() - Method in class htsjdk.variant.variantcontext.VariantContext
 
isTabix(String, String) - Method in class htsjdk.tribble.AbstractFeatureReader.ComponentMethods
 
isTransition(VariantContext) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Answers if the provided variant is transitional (otherwise, it's transversional).

isUnknownBases() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isUnset(int) - Method in enum htsjdk.samtools.SAMFlag
 
isUnsignedArray() - Method in class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue
 
isUnsignedArray() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
 
isUnsignedArray - Variable in class htsjdk.samtools.TagValueAndUnsignedArrayFlag
 
isUnsignedArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
 
isUnsignedArrayAttribute(String) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
isUrl(String) - Static method in class htsjdk.samtools.util.IOUtil

Returns true iff the string is a url.

isValid(String, long) - Method in class htsjdk.samtools.Cigar

Exhaustive validation of CIGAR.

isValid() - Method in class htsjdk.samtools.SAMRecord

Perform various validations of SAMRecord.

isValid(boolean) - Method in class htsjdk.samtools.SAMRecord

Perform various validations of SAMRecord.

isValid(String) - Static method in class htsjdk.samtools.sra.SRAAccession
 
isValid() - Method in class htsjdk.samtools.sra.SRAAccession
 
isValid(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
isValid() - Method in class htsjdk.tribble.index.interval.IntervalTree

Test code: make sure that the tree has all the properties
 defined by Red Black trees and interval trees
 
 o.

isValid() - Method in class htsjdk.variant.bcf2.BCF2Codec.SitesInfoForDecoding
 
isValidBase(byte) - Static method in class htsjdk.samtools.util.SequenceUtil

Returns true if the byte is in [acgtACGT].

isValidFile(InputStream) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
 
isValidUnsignedIntegerAttribute(long) - Static method in class htsjdk.samtools.SAMUtils

Checks if a long attribute value is within the allowed range of a 32-bit unsigned integer.

isVariant() - Method in class htsjdk.variant.variantcontext.VariantContext

convenience method for variants

isVendorFiltered() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
isVersionString(String) - Static method in enum htsjdk.variant.vcf.VCFHeaderVersion

are we a valid version string of some type

isWithinHammingDistance(String, String, int) - Static method in class htsjdk.samtools.util.StringUtil

Determines if two strings s1 and s2 are within maxHammingDistance of each other using the Hamming distance metric.

isWriteCommandLine() - Method in class htsjdk.variant.vcf.VCFHeader

If true, and isWriteEngineHeaders also returns true, the command line will be written to the VCF.

isWriteEngineHeaders() - Method in class htsjdk.variant.vcf.VCFHeader

If true additional engine headers will be written to the VCF, otherwise only the walker headers will be output.

isWriting() - Method in class htsjdk.samtools.util.BinaryCodec
 
IterableAdapter<T> - Class in htsjdk.samtools.util

Provides an adapter to wrap an Iterator with an Iterable, allowing it to be run through a foreach loop.

IterableAdapter(Iterator<T>) - Constructor for class htsjdk.samtools.util.IterableAdapter
 
IterableOnceIterator<T> - Class in htsjdk.samtools.util

Abstract implementation of an iterator that also implements Iterable (to return itself)
 so that it can be used if for() loops.

IterableOnceIterator() - Constructor for class htsjdk.samtools.util.IterableOnceIterator
 
Iterables - Class in htsjdk.samtools.util
 
iterateInSampleNameOrder(Iterable<String>) - Method in class htsjdk.variant.variantcontext.GenotypesContext

Iterate over the Genotypes in this context in the order specified by sampleNamesInOrder

iterateInSampleNameOrder() - Method in class htsjdk.variant.variantcontext.GenotypesContext

Iterate over the Genotypes in this context in their sample name order (A, B, C)
 regardless of the underlying order in the vector of genotypes

iterator() - Method in class htsjdk.samtools.BinList

Gets an iterator over all selected bins.

iterator() - Method in class htsjdk.samtools.BinningIndexContent.BinList
 
iterator() - Method in class htsjdk.samtools.Cigar

shortcut to getCigarElements().iterator()

iterator() - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap

Creates an iterator over all elements in map, in arbitrary order.

iterator(SAMFileSpan) - Method in class htsjdk.samtools.CRAMFileReader
 
iterator() - Method in class htsjdk.samtools.fastq.FastqReader

WARNING: Despite the fact that this class implements Iterable, calling iterator() method does not
 start iteration from the beginning of the file.

iterator() - Method in class htsjdk.samtools.reference.FastaSequenceIndex

Creates an iterator which can iterate through all entries in a fasta index.

iterator(SAMFileSpan) - Method in interface htsjdk.samtools.SamReader.Indexing

Iterate through the given chunks in the file.

iterator() - Method in interface htsjdk.samtools.SamReader

Iterate through file in order.

iterator() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
iterator(SAMFileSpan) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
iterator() - Method in class htsjdk.samtools.SAMRecordSetBuilder

Returns a CloseableIterator over the collection of SAMRecords.

iterator(SAMFileSpan) - Method in class htsjdk.samtools.SRAFileReader

Iterate through the given chunks in the file.

iterator() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
iterator() - Method in class htsjdk.samtools.util.DiskBackedQueue

Not supported at this time

iterator() - Method in class htsjdk.samtools.util.IntervalList

Returns an iterator over the intervals.

iterator() - Method in class htsjdk.samtools.util.IntervalTree

Return an iterator over the entire tree.

iterator(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Return an iterator over all intervals greater than or equal to the specified interval.

iterator() - Method in class htsjdk.samtools.util.IterableAdapter
 
iterator() - Method in class htsjdk.samtools.util.IterableOnceIterator

On the first call returns this object which is also an iterator.

iterator() - Method in class htsjdk.samtools.util.SortingCollection

Prepare to iterate through the records in order.

iterator() - Method in interface htsjdk.tribble.FeatureReader
 
iterator() - Method in class htsjdk.tribble.TabixFeatureReader
 
iterator() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
 
iterator() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator

function to satisfy the Iterable interface

iterator() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
iterator() - Method in class htsjdk.variant.vcf.VCFFileReader

Returns an iterator over all records in this VCF/BCF file.

ITF8 - Class in htsjdk.samtools.cram.io

Methods to read and write int values as per ITF8 specification in CRAM.

ITF8() - Constructor for class htsjdk.samtools.cram.io.ITF8
 




J

JavascriptSamRecordFilter - Class in htsjdk.samtools.filter

javascript based read filter
 
 
 The script puts the following variables in the script context:

 - 'record' a SamRecord (
 https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/
 SAMRecord.java ) - 'header' (
 https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/
 SAMFileHeader.java )

JavascriptSamRecordFilter(File, SAMFileHeader) - Constructor for class htsjdk.samtools.filter.JavascriptSamRecordFilter

constructor using a javascript File

JavascriptSamRecordFilter(String, SAMFileHeader) - Constructor for class htsjdk.samtools.filter.JavascriptSamRecordFilter

constructor using a javascript expression

JavascriptSamRecordFilter(Reader, SAMFileHeader) - Constructor for class htsjdk.samtools.filter.JavascriptSamRecordFilter

constructor using a java.io.Reader

JavascriptVariantFilter - Class in htsjdk.variant.variantcontext.filter

javascript based variant filter The script puts the following variables in
 the script context:

 - 'header' a htsjdk.variant.vcf.VCFHeader 
 - 'variant' a htsjdk.variant.variantcontext.VariantContext

JavascriptVariantFilter(File, VCFHeader) - Constructor for class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter

constructor using a javascript File

JavascriptVariantFilter(Reader, VCFHeader) - Constructor for class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter

constructor using a Reader

JavascriptVariantFilter(String, VCFHeader) - Constructor for class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter

constructor using a javascript expression

JexlMissingValueTreatment - Enum in htsjdk.variant.variantcontext

How to treat values that appear in a jexl expression but are missing in the context it's applied to

JexlVCMatchExp(String, Expression) - Constructor for class htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp

Create a new matcher expression with name and JEXL expression exp

join(Collection<?>, String) - Static method in class htsjdk.samtools.util.CollectionUtil

Construct a string by toString()ing each item in the collection with inBetween between each item.

join(String, Collection<T>) - Static method in class htsjdk.samtools.util.StringUtil
 
join(String, T...) - Static method in class htsjdk.samtools.util.StringUtil
 
join(String, Collection<T>) - Static method in class htsjdk.tribble.util.ParsingUtils
 
join(String, String[]) - Static method in class htsjdk.tribble.util.ParsingUtils

join an array of strings given a seperator

join(String, String[], int, int) - Static method in class htsjdk.tribble.util.ParsingUtils

join a set of strings, using the separator provided, from index start to index stop

join(String, Collection<T>) - Static method in class htsjdk.variant.utils.GeneralUtils

Returns a string of the form elt1.toString() [sep elt2.toString() ...





K

KEY_SEQUENCE_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
keySet() - Method in class htsjdk.samtools.util.Histogram

Returns the set of keys for this histogram.

keyType3Bytes - Variable in class htsjdk.samtools.cram.structure.ReadTag
 
keyType3BytesAsInt - Variable in class htsjdk.samtools.cram.structure.ReadTag
 
knownAtEof() - Method in class htsjdk.samtools.util.BinaryCodec
 




L

l - Variable in class htsjdk.tribble.util.TabixUtils.TIndex
 
landmarks - Variable in class htsjdk.samtools.cram.structure.Container
 
lastIndexOf(Object) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
Lazy<T> - Class in htsjdk.samtools.util

Simple utility for building an on-demand (lazy) object-initializer.

Lazy(Lazy.LazyInitializer<T>) - Constructor for class htsjdk.samtools.util.Lazy

Simple cons

Lazy.LazyInitializer<T> - Interface in htsjdk.samtools.util

Describes how to build the instance of the lazy object.

LAZY_NOW_LABEL - Static variable in class htsjdk.samtools.util.RelativeIso8601Date
 
LazyData(VCFHeader, int, byte[]) - Constructor for class htsjdk.variant.bcf2.BCF2Codec.LazyData
 
LazyData(ArrayList<Genotype>, List<String>, Map<String, Integer>) - Constructor for class htsjdk.variant.variantcontext.LazyGenotypesContext.LazyData
 
LazyGenotypesContext - Class in htsjdk.variant.variantcontext

Lazy-loading GenotypesContext.

LazyGenotypesContext(LazyGenotypesContext.LazyParser, Object, int) - Constructor for class htsjdk.variant.variantcontext.LazyGenotypesContext

Creates a new lazy loading genotypes context using the LazyParser to create
 genotypes data on demand.

LazyGenotypesContext.LazyData - Class in htsjdk.variant.variantcontext

Returns the data used in the full GenotypesContext constructor

 GenotypesContext.GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List)

LazyGenotypesContext.LazyParser - Interface in htsjdk.variant.variantcontext

Simple lazy parser interface.

LB - Variable in class htsjdk.samtools.SAMTagUtil
 
length() - Method in class htsjdk.samtools.fastq.FastqRecord

shortcut to getReadString().length()

length() - Method in class htsjdk.samtools.reference.ReferenceSequence

Gets the length of this reference sequence in bases.

length() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
 
length() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
length() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
length() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
length() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
 
length() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
length() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
 
length() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
 
length() - Method in class htsjdk.samtools.seekablestream.SeekableStream
 
length() - Method in class htsjdk.samtools.util.Interval

Gets the length of this interval.

length() - Method in class htsjdk.variant.variantcontext.Allele
 
less64(long, long) - Static method in class htsjdk.tribble.util.TabixUtils
 
lessExhaustivelyTestIndex(SamReader) - Static method in class htsjdk.samtools.BamIndexValidator

A less time-consuming index validation that only looks at the first and last references in the index
 and the first and last chunks in each of those

LEVEL_STARTS - Static variable in class htsjdk.samtools.GenomicIndexUtil

What is the starting bin for each level?

levenshteinDistance(String, String, int, int, int, int) - Static method in class htsjdk.samtools.util.StringUtil
 
LIBRARY_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
LiftOver - Class in htsjdk.samtools.liftover

Java port of UCSC liftOver.

LiftOver(File) - Constructor for class htsjdk.samtools.liftover.LiftOver

Load UCSC chain file in order to lift over Intervals.

liftOver(Interval) - Method in class htsjdk.samtools.liftover.LiftOver

Lift over the given interval to the new genome build using the liftOverMinMatch set for this
 LiftOver object.

liftOver(Interval, double) - Method in class htsjdk.samtools.liftover.LiftOver

Lift over the given interval to the new genome build.

LiftOver.PartialLiftover - Class in htsjdk.samtools.liftover

Represents a portion of a liftover operation, for use in diagnosing liftover failures.

LinearIndex - Class in htsjdk.samtools

The linear index associated with a given reference in a BAM index.

LinearIndex(int, int, long[]) - Constructor for class htsjdk.samtools.LinearIndex
 
LinearIndex - Class in htsjdk.tribble.index.linear

Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in
 genomic coordinates).

LinearIndex(List<LinearIndex.ChrIndex>, File) - Constructor for class htsjdk.tribble.index.linear.LinearIndex

Initialize using the specified indices

LinearIndex(String) - Constructor for class htsjdk.tribble.index.linear.LinearIndex

Initialize with default parameters

LinearIndex(InputStream) - Constructor for class htsjdk.tribble.index.linear.LinearIndex

Load from file.

LinearIndex.ChrIndex - Class in htsjdk.tribble.index.linear

Blocks are organized as a simple flat list:
 
 Block 0
 Block 1
 Block 2
 

 There's a constant bin width, so that each block corresponds to a specific interval
 over the genome based on its index, as in:
 

 Block 0: (0 - binWidth]
 Block 1: (binWidth - 2 * binWidth]
 Block 2: (2 * binWidth - 3 * binWidth]
 

 Note that covered regions are open on the left ( and closed on the right ].

LinearIndexCreator - Class in htsjdk.tribble.index.linear

For creating a LinearIndex from a stream of features.

LinearIndexCreator(File, int) - Constructor for class htsjdk.tribble.index.linear.LinearIndexCreator
 
LinearIndexCreator(File) - Constructor for class htsjdk.tribble.index.linear.LinearIndexCreator
 
LineIterator - Interface in htsjdk.tribble.readers

A very simple descriptor for line-iterables.

LineIteratorImpl - Class in htsjdk.tribble.readers

A simple iterator over the elements in LineReader.

LineIteratorImpl(LineReader) - Constructor for class htsjdk.tribble.readers.LineIteratorImpl
 
lineNo - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
LineReader - Interface in htsjdk.samtools.util

Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else.

LineReader - Interface in htsjdk.tribble.readers

Interface for line-oriented readers.

LineReaderUtil - Class in htsjdk.tribble.readers

Deprecated.

LineReaderUtil() - Constructor for class htsjdk.tribble.readers.LineReaderUtil

Deprecated.
 
LineReaderUtil.LineReaderOption - Enum in htsjdk.tribble.readers

Deprecated.

listIterator() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
listIterator(int) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
ListMap<K,V> - Class in htsjdk.samtools.util

A Map class that holds a list of entries under each key instead of a single entry, and
 provides utility methods for adding an entry under a key.

ListMap() - Constructor for class htsjdk.samtools.util.ListMap
 
LittleEndianInputStream - Class in htsjdk.tribble.util

Input stream with methods to convert byte arrays to numeric values using "little endian" order.

LittleEndianInputStream(InputStream) - Constructor for class htsjdk.tribble.util.LittleEndianInputStream
 
LittleEndianOutputStream - Class in htsjdk.tribble.util
 
LittleEndianOutputStream(OutputStream) - Constructor for class htsjdk.tribble.util.LittleEndianOutputStream
 
loadIndex(File, FeatureCodec) - Static method in class htsjdk.tribble.example.CountRecords
 
loadIndex(String) - Static method in class htsjdk.tribble.example.IndicesAreEqual
 
loadIndex(String) - Static method in class htsjdk.tribble.index.IndexFactory

Load in index from the specified file.

loadSequenceDictionary() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
loc(String, long, long) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells us that the resulting VariantContext should have the specified location

Locatable - Interface in htsjdk.samtools.util

Any class that has a single logical mapping onto the genome should implement Locatable
 positions should be reported as 1-based and closed at both ends

LocationAware - Interface in htsjdk.samtools.util

Describes API for getting current position in a stream, writer, or underlying file.

locParts - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
Locus - Interface in htsjdk.samtools.util

Location info about a locus.

LocusComparator<T extends Locus> - Class in htsjdk.samtools.util

compares first by sequence index then by position

LocusComparator() - Constructor for class htsjdk.samtools.util.LocusComparator
 
LocusImpl - Class in htsjdk.samtools.util

Simple implementation of Locus interface for ease of passing as an arg and comparing with other Locus implementations.

LocusImpl(int, int) - Constructor for class htsjdk.samtools.util.LocusImpl
 
LocusInfo(SAMSequenceRecord, int) - Constructor for class htsjdk.samtools.util.SamLocusIterator.LocusInfo
 
log(String...) - Method in class htsjdk.samtools.util.AbstractProgressLogger

Log a message to whatever logger is being used

Log - Class in htsjdk.samtools.util

A wafer thin wrapper around System.err that uses var-args to make it
 much more efficient to call the logging methods in without having to
 surround every call site with calls to Log.isXXXEnabled().

log(String...) - Method in class htsjdk.samtools.util.ProgressLogger
 
Log.LogLevel - Enum in htsjdk.samtools.util

Enumeration for setting log levels.

LOG10_P_OF_ZERO - Static variable in class htsjdk.variant.utils.GeneralUtils

The smallest log10 value we'll emit from normalizeFromLog10 and other functions
 where the real-space value is 0.0.

log10PError(double) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Set the GQ with a log10PError value

log10PError(double) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells us that the resulting VariantContext should have log10PError

login(String, String) - Method in class htsjdk.samtools.util.ftp.FTPClient

Wrapper for the commands user [username] and pass
 [password].

LongLineBufferedReader - Class in htsjdk.tribble.readers

A variant of BufferedReader with improved performance reading files with long lines.

LongLineBufferedReader(Reader, int) - Constructor for class htsjdk.tribble.readers.LongLineBufferedReader

Creates a buffering character-input stream that uses an input buffer of
 the specified size.

LongLineBufferedReader(Reader) - Constructor for class htsjdk.tribble.readers.LongLineBufferedReader

Creates a buffering character-input stream that uses a default-sized
 input buffer.

lower_than_mapping_score(int) - Static method in class htsjdk.samtools.cram.lossy.ReadCategory
 
lowerThanCoverage(int) - Static method in class htsjdk.samtools.cram.lossy.BaseCategory
 
LTF8 - Class in htsjdk.samtools.cram.io

Methods to read and write LTF8 as per CRAM specs.

LTF8() - Constructor for class htsjdk.samtools.cram.io.LTF8
 




M

MAGIC - Static variable in class htsjdk.samtools.cram.structure.CramHeader
 
magic - Variable in enum htsjdk.samtools.SamIndexes
 
MAGIC_HEADER_START - Static variable in class htsjdk.variant.bcf2.BCFVersion

BCF2 begins with the MAGIC info BCF_M_m where M is the major version (currently 2)
 and m is the minor version, currently 1

MAGIC_NUMBER - Static variable in class htsjdk.tribble.index.AbstractIndex
 
MAGIC_NUMBER - Static variable in class htsjdk.tribble.index.tabix.TabixIndex
 
main(String[]) - Static method in class htsjdk.samtools.apps.TimeChannel
 
main(String[]) - Static method in class htsjdk.samtools.apps.TimeRandomAccessFile
 
main(String[]) - Static method in class htsjdk.samtools.example.PrintReadsExample
 
main(String[]) - Static method in class htsjdk.samtools.FixBAMFile
 
main(String[]) - Static method in class htsjdk.samtools.SAMTools
 
main(String[]) - Static method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
main(String[]) - Static method in class htsjdk.samtools.util.DateParser
 
main(String[]) - Static method in class htsjdk.samtools.util.HttpUtils
 
main(String[]) - Static method in class htsjdk.tribble.example.CountRecords

The main method of this class:
  1) checks to see that the feature file exists
  2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk
  3) creates a FeatureSource
  4) iterates over the records, emitting a final tally for the number of features seen

main(String[]) - Static method in class htsjdk.tribble.example.IndexToTable

this class:
  1) checks to see that the feature file exists
  2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk
  3) Converts the index to a human readable table

main(String[]) - Static method in class htsjdk.tribble.example.IndicesAreEqual
 
main(String[]) - Static method in class htsjdk.tribble.example.ProfileIndexReading

This class times the loading of an index file a number of times,
 and prints the result of each trial

main(String[]) - Static method in class htsjdk.tribble.readers.AsciiLineReader
 
main(String[]) - Static method in class htsjdk.tribble.readers.PositionalBufferedStream
 
main(String[]) - Static method in class htsjdk.tribble.readers.TabixReader
 
main(String[]) - Static method in class htsjdk.variant.example.PrintVariantsExample
 
major - Variable in class htsjdk.samtools.cram.common.Version
 
MAJOR_HEADER_PREFIX - Static variable in class htsjdk.samtools.metrics.MetricsFile
 
make(Iterator<SAMRecord>, DownsamplingIteratorFactory.Strategy, double, double, int) - Static method in class htsjdk.samtools.DownsamplingIteratorFactory

Creates a new DownsamplingIterator using the supplied Strategy that attempts to read from the provided iterator and return
 approximately proportion of the records read.

make(File, DownsamplingIteratorFactory.Strategy, double, double, int) - Static method in class htsjdk.samtools.DownsamplingIteratorFactory

Convenience method that constructs a downsampling iterator for all the reads in a SAM file.

make(SamReader, DownsamplingIteratorFactory.Strategy, double, double, int) - Static method in class htsjdk.samtools.DownsamplingIteratorFactory

Convenience method that constructs a downsampling iterator for all the reads available from a SamReader.

make() - Static method in class htsjdk.samtools.SamReaderFactory

Creates an "empty" factory with no enabled SamReaderFactory.Options, ValidationStringency.DEFAULT_STRINGENCY, and
 DefaultSAMRecordFactory.

make(K) - Method in interface htsjdk.samtools.util.CollectionUtil.DefaultingMap.Factory
 
make() - Method in interface htsjdk.samtools.util.Lazy.LazyInitializer

Returns the desired object instance.

make() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Create a new Genotype object using the values set in this builder.

make() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Takes all of the builder data provided up to this point, and instantiates
 a freshly allocated VariantContext with all of the builder data.

make(boolean) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
 
makeBAMWriter(SAMFileHeader, boolean, File) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a BAMFileWriter that is ready to receive SAMRecords.

makeBAMWriter(SAMFileHeader, boolean, File, int) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a BAMFileWriter that is ready to receive SAMRecords.

makeBAMWriter(SAMFileHeader, boolean, OutputStream) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords.

makeBinaryTag(String) - Method in class htsjdk.samtools.SAMTagUtil

Convert from String representation of tag name to short representation.

makeCigarStringWithIndelPossibleClipping(int, int, int, int, int) - Static method in class htsjdk.samtools.util.SequenceUtil

Create a cigar string for a gapped alignment, which may have soft clipping at either end

makeCigarStringWithPossibleClipping(int, int, int) - Static method in class htsjdk.samtools.util.SequenceUtil

Create a simple ungapped cigar string, which might have soft clipping at either end

makeCollection(Iterator<T>) - Static method in class htsjdk.samtools.util.CollectionUtil
 
makeContigHeaderLines(SAMSequenceDictionary, File) - Static method in class htsjdk.variant.vcf.VCFUtils

Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null

makeCRAMWriter(SAMFileHeader, OutputStream, File) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a CRAMFileWriter on an output stream.

makeCRAMWriter(SAMFileHeader, File, File) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a CRAMFileWriter on an output file.

makeCRAMWriter(SAMFileHeader, boolean, File, File) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a CRAMFileWriter on an output file.

makeDefault() - Static method in class htsjdk.samtools.SamReaderFactory

Creates a copy of the default SamReaderFactory.

makeDeflater(int, boolean) - Method in class htsjdk.samtools.util.zip.DeflaterFactory

Returns a deflater object that will be used when writing BAM files.

makeDictionary(VCFHeader) - Static method in class htsjdk.variant.bcf2.BCF2Utils

Create a strings dictionary from the VCF header

 The dictionary is an ordered list of common VCF identifers (FILTER, INFO, and FORMAT)
 fields.

makeFileNameSafe(String) - Static method in class htsjdk.samtools.util.IOUtil

Takes a string and replaces any characters that are not safe for filenames with an underscore

makeIndexableSourceFromStream(InputStream) - Method in class htsjdk.tribble.AsciiFeatureCodec
 
makeIndexableSourceFromStream(InputStream) - Method in class htsjdk.tribble.BinaryFeatureCodec

PositionalBufferedStream is already LocationAware.

makeIndexableSourceFromStream(InputStream) - Method in interface htsjdk.tribble.FeatureCodec

Generates a LocationAware reader of type SOURCE.

makeList(T...) - Static method in class htsjdk.samtools.util.CollectionUtil
 
makePermutations(List<T>, int, boolean) - Static method in class htsjdk.variant.utils.GeneralUtils

Make all combinations of N size of objects

 if objects = [A, B, C]
 if N = 1 => [[A], [B], [C]]
 if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]]

makeReadUnmapped(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Strip mapping information from a SAMRecord.

makeReadUnmappedWithOriginalTags(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Strip mapping information from a SAMRecord, but preserve it in the 'O' tags if it isn't already set.

makeReferenceFromAlignment(SAMRecord, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil

Produce reference bases from an aligned SAMRecord with MD string and Cigar.

makeSAMOrBAMWriter(SAMFileHeader, boolean, File) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create either a SAM or a BAM writer based on examination of the outputFile extension.

makeSamRecordIntervalIterator(SamReader, List<Interval>, boolean) - Method in class htsjdk.samtools.util.SamRecordIntervalIteratorFactory
 
makeSAMWriter(SAMFileHeader, boolean, File) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a SAMTextWriter that is ready to receive SAMRecords.

makeSAMWriter(SAMFileHeader, boolean, OutputStream) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a SAMTextWriter for writing to a stream that is ready to receive SAMRecords.

makeSet(T...) - Static method in class htsjdk.samtools.util.CollectionUtil
 
makeSoftClipCigar(int) - Static method in class htsjdk.samtools.util.SequenceUtil
 
makeSourceFromStream(InputStream) - Method in class htsjdk.tribble.AsciiFeatureCodec
 
makeSourceFromStream(InputStream) - Method in class htsjdk.tribble.BinaryFeatureCodec
 
makeSourceFromStream(InputStream) - Method in interface htsjdk.tribble.FeatureCodec

Generates a reader of type SOURCE appropriate for use by this codec from the generic input stream.

makeStringTag(short) - Method in class htsjdk.samtools.SAMTagUtil

Convert from short representation of tag name to String representation.

makeValue(Key) - Method in interface htsjdk.samtools.util.ResourceLimitedMapFunctor

Create a new value corresponding to the key

makeWithShallowCopy() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Create a new Genotype object using the values set in this builder, and perform a
 shallow copy of reference types to allow safer re-use of this builder

 After creation the values in this builder can be modified and more Genotypes
 created.

makeWriter(SAMFileHeader, boolean, File, File) - Method in class htsjdk.samtools.SAMFileWriterFactory

Create a SAM, BAM or CRAM writer based on examination of the outputFile extension.

MalformedFeatureFile(String, String, Exception) - Constructor for exception htsjdk.tribble.TribbleException.MalformedFeatureFile
 
MalformedFeatureFile(String, String) - Constructor for exception htsjdk.tribble.TribbleException.MalformedFeatureFile
 
MAPPING_QUALITY_ZERO_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
mappingQuality - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
MappingQualityFilter - Class in htsjdk.samtools.filter

Filter things with low mapping quality.

MappingQualityFilter(int) - Constructor for class htsjdk.samtools.filter.MappingQualityFilter
 
mappingQualityScoreCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
mappingScoreCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
mark(int) - Method in class htsjdk.samtools.cram.io.CountingInputStream
 
mark(int) - Method in class htsjdk.samtools.cram.io.CRC32InputStream
 
mark(int) - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
 
mark(int) - Method in class htsjdk.tribble.readers.LongLineBufferedReader

Marks the present position in the stream.

markSupported() - Method in class htsjdk.samtools.cram.io.CountingInputStream
 
markSupported() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
 
markSupported() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
 
markSupported() - Method in class htsjdk.tribble.readers.LongLineBufferedReader

Tells whether this stream supports the mark() operation, which it does.

match() - Static method in class htsjdk.samtools.cram.lossy.BaseCategory
 
match(VariantContext, VariantContextUtils.JexlVCMatchExp) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Returns true if exp match vc.

match(VariantContext, Collection<VariantContextUtils.JexlVCMatchExp>) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Matches each VariantContextUtils.JexlVCMatchExp exp against the data contained in vc,
 and returns a map from these expressions to true (if they matched) or false (if they didn't).

match(VariantContext, Genotype, VariantContextUtils.JexlVCMatchExp) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Returns true if exp match vc, g.

match(VariantContext, Genotype, VariantContextUtils.JexlVCMatchExp, JexlMissingValueTreatment) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Returns true if exp match vc, g.

match(VariantContext, Genotype, Collection<VariantContextUtils.JexlVCMatchExp>) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Matches each VariantContextUtils.JexlVCMatchExp exp against the data contained in vc, g,
 and returns a map from these expressions to true (if they matched) or false (if they didn't).

match(VariantContext, Genotype, Collection<VariantContextUtils.JexlVCMatchExp>, JexlMissingValueTreatment) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Matches each VariantContextUtils.JexlVCMatchExp exp against the data contained in vc, g,
 and returns a map from these expressions to true (if they matched) or false (if they didn't).

MATCH_OR_MISMATCH - Static variable in enum htsjdk.samtools.CigarOperator
 
MATE_STRAND_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
MATE_UNMAPPED_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
mateAlignmentStart - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
mateAlignmentStartCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
mateBitFlagCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
mateBitFlagsCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
mateFlags - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
mateReferenceIdCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
mateSequenceID - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
MathUtils - Class in htsjdk.tribble.util

a collection of functions and classes for various common calculations

MathUtils() - Constructor for class htsjdk.tribble.util.MathUtils
 
MathUtils.RunningStat - Class in htsjdk.tribble.util

a class for calculating moving statistics - this class returns the
 mean, variance, and std dev after accumulating any number of records.

max() - Method in class htsjdk.samtools.util.IntervalTree

Find the greatest interval in the tree.

max(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Find the latest interval in the tree less than or equal to the specified interval.

MAX_ALLELE_SIZE_BEFORE_WARNING - Static variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
MAX_ALLELES_IN_GENOTYPES - Static variable in class htsjdk.variant.bcf2.BCF2Utils
 
MAX_BINS - Static variable in class htsjdk.samtools.GenomicIndexUtil

Reports the maximum number of bins that can appear in a binning index.

MAX_BLOCK_ADDRESS - Static variable in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
 
MAX_COMPRESSED_BLOCK_SIZE - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED - Static variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods

The maximum number of diploid alternate alleles that we can represent as genotype likelihoods

MAX_FEATURES_PER_BIN - Static variable in class htsjdk.tribble.index.linear.LinearIndex
 
MAX_GENOTYPE_QUAL - Static variable in class htsjdk.variant.vcf.VCFConstants
 
MAX_INLINE_ELEMENTS - Static variable in class htsjdk.variant.bcf2.BCF2Utils
 
MAX_INSERT_SIZE - Static variable in class htsjdk.samtools.SAMRecord

abs(insertSize) must be <= this

MAX_ITEMS_IN_RAM - Static variable in class htsjdk.samtools.util.SortingLongCollection
 
MAX_LINEAR_INDEX_SIZE - Static variable in class htsjdk.samtools.GenomicIndexUtil
 
MAX_LINEAR_INDEX_SIZE - Static variable in class htsjdk.samtools.LinearIndex
 
MAX_OFFSET - Static variable in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
 
MAX_PHRED_SCORE - Static variable in class htsjdk.samtools.SAMUtils
 
MAX_PL - Static variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
MAX_QUALITY - Static variable in class htsjdk.samtools.SQTagUtil
 
MAX_UBYTE - Static variable in class htsjdk.samtools.util.BinaryCodec
 
MAX_UINT - Static variable in class htsjdk.samtools.util.BinaryCodec
 
MAX_USHORT - Static variable in class htsjdk.samtools.util.BinaryCodec
 
maxAttributes(int) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Tell's this builder that we have at most these number of attributes

maxBinNumber - Variable in class htsjdk.samtools.BinningIndexContent.BinList
 
maxElementIndex(double[]) - Static method in class htsjdk.variant.utils.GeneralUtils
 
maxElementIndex(double[], int) - Static method in class htsjdk.variant.utils.GeneralUtils
 
maxIntegerType(BCF2Type, BCF2Type) - Static method in class htsjdk.variant.bcf2.BCF2Utils

Returns the maximum BCF2 integer size of t1 and t2

 For example, if t1 == INT8 and t2 == INT16 returns INT16

maybeBgzfWrapOutputStream(File, OutputStream) - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream
 
maybeBufferedSeekableStream(SeekableStream, int) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferedSeekableStream(SeekableStream) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferedSeekableStream(File) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferedSeekableStream(URL) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferInputStream(InputStream) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferInputStream(InputStream, int) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferOutputStream(OutputStream) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferOutputStream(OutputStream, int) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferReader(Reader, int) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferReader(Reader) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferWriter(Writer, int) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeBufferWriter(Writer) - Static method in class htsjdk.samtools.util.IOUtil
 
maybeOpen(URL) - Method in class htsjdk.samtools.CustomReaderFactory

Check if the url is supposed to be handled by the custom factory and if so
 attempt to create reader via an instance of this custom factory.

MC - Variable in class htsjdk.samtools.SAMTagUtil
 
MD - Variable in class htsjdk.samtools.SAMTagUtil
 
md5() - Method in class htsjdk.samtools.SAMSequenceDictionary

return a MD5 sum for ths dictionary, the checksum is re-computed each
 time this method is called.

md5() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
 
md5() - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
 
MD5_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
 
Md5CalculatingInputStream - Class in htsjdk.samtools.util

Class to generate an MD5 string for a file as it is being read

Md5CalculatingInputStream(InputStream, File) - Constructor for class htsjdk.samtools.util.Md5CalculatingInputStream

Constructor that takes in the InputStream that we are wrapping
 and creates the MD5 MessageDigest

Md5CalculatingOutputStream - Class in htsjdk.samtools.util

Class to generate an MD5 string for a file as it is being read

Md5CalculatingOutputStream(OutputStream, File) - Constructor for class htsjdk.samtools.util.Md5CalculatingOutputStream

Constructor that takes in the OutputStream that we are wrapping
 and creates the MD5 MessageDigest

mean() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
 
merge(BAMFileSpan[]) - Static method in class htsjdk.samtools.BAMFileSpan
 
mergeDictionaries(SAMSequenceDictionary, SAMSequenceDictionary, List<String>) - Static method in class htsjdk.samtools.SAMSequenceDictionary

Will merge dictionaryTags from two dictionaries into one focusing on merging the tags rather than the sequences.

MergingIterator<T> - Class in htsjdk.samtools.util

An iterator over Iterators that return Ts.

MergingIterator(Comparator<T>, Collection<CloseableIterator<T>>) - Constructor for class htsjdk.samtools.util.MergingIterator

Creates a MergingIterator over the given Collection of iterators whose elements will be
 returned in the order defined by the given Comparator.

MergingSamRecordIterator - Class in htsjdk.samtools

Provides an iterator interface for merging multiple underlying iterators into a single
 iterable stream.

MergingSamRecordIterator(SamFileHeaderMerger, boolean) - Constructor for class htsjdk.samtools.MergingSamRecordIterator

Deprecated.
replaced by MergingSamRecordIterator.MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)


MergingSamRecordIterator(SamFileHeaderMerger, Collection<SamReader>, boolean) - Constructor for class htsjdk.samtools.MergingSamRecordIterator

Constructs a new merging iterator with the same set of readers and sort order as
 provided by the header merger parameter.

MergingSamRecordIterator(SamFileHeaderMerger, Map<SamReader, CloseableIterator<SAMRecord>>, boolean) - Constructor for class htsjdk.samtools.MergingSamRecordIterator

Add a set of SAM file iterators to the merging iterator.

metaCharacter - Variable in class htsjdk.tribble.index.tabix.TabixFormat

Lines in the file being indexed that start with this character are ignored.

METADATA_INDICATOR - Static variable in class htsjdk.variant.vcf.VCFHeader
 
METRIC_HEADER - Static variable in class htsjdk.samtools.metrics.MetricsFile
 
MetricBase - Class in htsjdk.samtools.metrics

A base class from which all Metric classes should inherit.

MetricBase() - Constructor for class htsjdk.samtools.metrics.MetricBase
 
MetricsFile<BEAN extends MetricBase,HKEY extends java.lang.Comparable> - Class in htsjdk.samtools.metrics

Contains a set of metrics that can be written to a file and parsed back
 again.

MetricsFile() - Constructor for class htsjdk.samtools.metrics.MetricsFile
 
MF - Variable in class htsjdk.samtools.SAMTagUtil
 
min() - Method in class htsjdk.samtools.util.IntervalTree

Find the least interval in the tree.

min(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Find the earliest interval in the tree greater than or equal to the specified interval.

mIndex - Variable in class htsjdk.tribble.readers.TabixReader
 
minor - Variable in class htsjdk.samtools.cram.common.Version
 
MINOR_HEADER_PREFIX - Static variable in class htsjdk.samtools.metrics.MetricsFile
 
minOverlapper(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Find the earliest interval in the tree that overlaps the specified interval.

mismatch() - Static method in class htsjdk.samtools.cram.lossy.BaseCategory
 
mismatchesAt(int) - Method in class htsjdk.samtools.cram.ref.ReferenceTracks
 
MISSING_DEPTH_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
MISSING_GENOTYPE_QUALITY_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
MISSING_HAPLOTYPE_QUALITY_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
MISSING_QUALITY_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
MISSING_QUALITY_v3_DOUBLE - Static variable in class htsjdk.variant.vcf.VCFConstants
 
MISSING_VALUE_v4 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
mMateReferenceIndex - Variable in class htsjdk.samtools.SAMRecord
 
modifyOption(Options, boolean) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set or unset option depending on the boolean given

MQ - Variable in class htsjdk.samtools.SAMTagUtil
 
mReferenceIndex - Variable in class htsjdk.samtools.SAMRecord
 
MULTI_REFERENCE - Static variable in class htsjdk.samtools.cram.structure.Slice
 
MultiMap() - Constructor for class htsjdk.samtools.util.CollectionUtil.MultiMap
 
Murmur3 - Class in htsjdk.samtools.util

Provides an implementation of the Murmur3_32 hash algorithm that has desirable properties in terms of randomness
 and uniformity of the distribution of output values that make it a useful hashing algorithm for downsampling.

Murmur3(int) - Constructor for class htsjdk.samtools.util.Murmur3

Constructs a Murmur3 hash with the given seed.

MutableIndex - Interface in htsjdk.tribble.index

Some Index implementations can be modified in memory.

MutableInt - Class in htsjdk.samtools.cram.common
 
MutableInt() - Constructor for class htsjdk.samtools.cram.common.MutableInt
 
myIndexSeekableStream() - Static method in class htsjdk.samtools.example.ExampleSamUsage
 




N

n - Static variable in class htsjdk.samtools.util.SequenceUtil

Byte typed variables for all normal bases.

N - Static variable in class htsjdk.samtools.util.SequenceUtil

Byte typed variables for all normal bases.

name(String) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Set this genotype's name

name - Variable in class htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
 
name - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
name3BytesToInt(byte[]) - Static method in class htsjdk.samtools.cram.structure.ReadTag
 
NameAwareCodec - Interface in htsjdk.tribble

Created by IntelliJ IDEA.

nameType3BytesToInt(String, char) - Static method in class htsjdk.samtools.cram.structure.ReadTag
 
nanos - Variable in class htsjdk.samtools.cram.encoding.reader.DataReaderFactory.DataReaderWithStats
 
newInstance(SortingCollection.Codec<T>, int, List<File>) - Static method in class htsjdk.samtools.util.DiskBackedQueue

Syntactic sugar around the ctor, to save some typing of type parameters

newInstance(Class<T>, SortingCollection.Codec<T>, Comparator<T>, int, File...) - Static method in class htsjdk.samtools.util.SortingCollection

Syntactic sugar around the ctor, to save some typing of type parameters

newInstance(Class<T>, SortingCollection.Codec<T>, Comparator<T>, int, Collection<File>) - Static method in class htsjdk.samtools.util.SortingCollection

Syntactic sugar around the ctor, to save some typing of type parameters

newInstance(Class<T>, SortingCollection.Codec<T>, Comparator<T>, int) - Static method in class htsjdk.samtools.util.SortingCollection

Syntactic sugar around the ctor, to save some typing of type parameters.

newTempFile(String, String, File[], long) - Static method in class htsjdk.samtools.util.IOUtil

Creates a new tmp file on one of the available temp filesystems, registers it for deletion
 on JVM exit and then returns it.

newTempFile(String, String, File[]) - Static method in class htsjdk.samtools.util.IOUtil

Creates a new tmp file on one of the potential filesystems that has at least 5GB free.

newWriter(File) - Method in class htsjdk.samtools.fastq.FastqWriterFactory
 
next() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
 
next() - Method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
 
next - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
next() - Method in class htsjdk.samtools.CRAMIterator
 
next() - Method in class htsjdk.samtools.DuplicateSetIterator
 
next() - Method in class htsjdk.samtools.fastq.FastqReader
 
next() - Method in class htsjdk.samtools.filter.FilteringSamIterator

Returns the next element in the iteration.

next() - Method in class htsjdk.samtools.MergingSamRecordIterator

Returns the next record from the top most iterator during merging.

next - Variable in class htsjdk.samtools.SAMBinaryTagAndValue
 
next() - Method in class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
 
next() - Method in class htsjdk.samtools.SamReader.AssertingIterator
 
next() - Method in class htsjdk.samtools.sra.SRAAlignmentIterator
 
next() - Method in class htsjdk.samtools.sra.SRAUnalignmentIterator
 
next() - Method in class htsjdk.samtools.SRAIterator

Call hasNext to make sure that one of inner iterators points to the next record, the retrieve the record from
 one of them.

next - Variable in class htsjdk.samtools.util.AbstractIterator
 
next() - Method in class htsjdk.samtools.util.AbstractIterator
 
next() - Method in class htsjdk.samtools.util.AbstractLocusIterator

hasNext() has been fixed so that if it returns true, next() is now guaranteed not to return null.

next() - Method in class htsjdk.samtools.util.AsyncBufferedIterator
 
next() - Method in class htsjdk.samtools.util.DelegatingIterator
 
next() - Method in class htsjdk.samtools.util.IntervalTree.FwdIterator
 
next() - Method in class htsjdk.samtools.util.IntervalTree.OverlapIterator
 
next() - Method in class htsjdk.samtools.util.IntervalTree.RevIterator
 
next() - Method in class htsjdk.samtools.util.IntervalTree.ValuesIterator
 
next() - Method in class htsjdk.samtools.util.MergingIterator
 
next() - Method in class htsjdk.samtools.util.PeekableIterator

Returns the next object and advances the iterator.

next() - Method in class htsjdk.samtools.util.PeekIterator
 
next() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer

Returns the next element in the iteration.

next() - Method in class htsjdk.samtools.util.SortingLongCollection

Call only if hasNext() == true.

next() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
 
next() - Method in interface htsjdk.tribble.readers.TabixReader.Iterator

return null when there is no more data to read

next() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator

Returns the next element in the iteration.

nextFragmentAlignmentStart - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
nextFragmentReferenceSequenceIDCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
nextPosition(int, int) - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask

It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

nextPosition(int, int) - Method in interface htsjdk.samtools.util.ReferenceSequenceMask

It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

nextPosition(int, int) - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
 
nextSequence() - Method in class htsjdk.samtools.reference.FastaSequenceFile
 
nextSequence() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile

Gets the next sequence if available, or null if not present.

nextSequence() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile

Retrieves the next whole sequences from the file.

nextSequence() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
nGenotypeFields - Variable in class htsjdk.variant.bcf2.BCF2Codec.LazyData
 
NH - Variable in class htsjdk.samtools.SAMTagUtil
 
NM - Static variable in class htsjdk.samtools.ReservedTagConstants

Number of nucleotide differences (Specified in the SAM spec doc)

NM - Variable in class htsjdk.samtools.SAMTagUtil
 
NO_ALIGNMENT_CIGAR - Static variable in class htsjdk.samtools.SAMRecord

Cigar string for an unaligned read.

NO_ALIGNMENT_REFERENCE_INDEX - Static variable in class htsjdk.samtools.SAMRecord

If a read has this reference index, it is unaligned, but not all unaligned reads have
 this reference index (see above).

NO_ALIGNMENT_REFERENCE_NAME - Static variable in class htsjdk.samtools.SAMRecord

If a read has this reference name, it is unaligned, but not all unaligned reads have
 this reference name (see above).

NO_ALIGNMENT_SPAN - Static variable in class htsjdk.samtools.cram.structure.Slice
 
NO_ALIGNMENT_START - Static variable in class htsjdk.samtools.cram.structure.Slice
 
NO_ALIGNMENT_START - Static variable in class htsjdk.samtools.SAMRecord

If a read has reference name "*", it will have this value for position.

NO_CALL - Static variable in class htsjdk.variant.variantcontext.Allele
 
NO_CALL_ALLELE - Static variable in class htsjdk.variant.vcf.VCFConstants
 
NO_CALL_STRING - Static variable in class htsjdk.variant.variantcontext.Allele

A generic static NO_CALL allele for use

NO_CODE - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
NO_COMPRESSION_OVERHEAD - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
 
NO_GENOTYPES - Static variable in class htsjdk.variant.variantcontext.GenotypesContext

static constant value for an empty GenotypesContext.

NO_GENOTYPES - Static variable in class htsjdk.variant.variantcontext.VariantContext
 
NO_HEADER_END - Static variable in class htsjdk.tribble.FeatureCodecHeader

The value of the headerEnd field when there's no header

NO_LOG10_PERROR - Static variable in class htsjdk.variant.variantcontext.CommonInfo
 
NO_LOG10_PERROR - Static variable in class htsjdk.variant.variantcontext.VariantContext
 
NO_MAPPING_QUALITY - Static variable in class htsjdk.samtools.SAMRecord

Alignment score for an unaligned read.

NO_OPTIONS - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
 
NO_OPTIONS - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.
 
noAD() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

This genotype has no AD value

noAttributes() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Tells this builder to remove all extended attributes

noDP() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

This genotype has no DP value

nofBlocks - Variable in class htsjdk.samtools.cram.structure.Slice
 
nofRecords - Variable in class htsjdk.samtools.cram.structure.Container
 
nofRecords - Variable in class htsjdk.samtools.cram.structure.Slice
 
noGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells this builder that the resulting VariantContext should not contain any GenotypeContext

noGQ() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

This genotype has no GQ value

noID() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells us that the resulting VariantContext should not have an ID

NON_ZERO_BUFFER_SIZE - Static variable in class htsjdk.samtools.Defaults

Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero.

noPL() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

This genotype has no PL value

normalize(ArrayList<CramCompressionRecord>, byte[], int, SubstitutionMatrix) - Method in class htsjdk.samtools.cram.build.CramNormalizer
 
normalizeBase(byte) - Static method in class htsjdk.samtools.cram.build.Utils

CRAM operates with upper case bases, so both read and ref bases should be
 upper-cased and vocab controlled.

normalizeFromLog10(double[]) - Static method in class htsjdk.variant.utils.GeneralUtils

normalizes the log10-based array.

normalizeFromLog10(double[], boolean) - Static method in class htsjdk.variant.utils.GeneralUtils

normalizes the log10-based array.

normalizeFromLog10(double[], boolean, boolean) - Static method in class htsjdk.variant.utils.GeneralUtils

See #normalizeFromLog10 but with the additional option to use an approximation that keeps the calculation always in log-space

NOT_PRIMARY_ALIGNMENT_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
noteCurrentRecord(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
 
NotPrimaryAlignmentFilter - Class in htsjdk.samtools.filter

Filter out SAMRecords with NotPrimaryAlignment flag set

 $Id$

NotPrimaryAlignmentFilter() - Constructor for class htsjdk.samtools.filter.NotPrimaryAlignmentFilter
 
NotPrimarySkippingIterator - Class in htsjdk.samtools

Wrapper around SAMRecord iterator that skips over non-primary elements.

NotPrimarySkippingIterator(CloseableIterator<SAMRecord>) - Constructor for class htsjdk.samtools.NotPrimarySkippingIterator
 
notToBeDirectlyAccessedGenotypes - Variable in class htsjdk.variant.variantcontext.GenotypesContext

An ArrayList of genotypes contained in this context

 WARNING: TO ENABLE THE LAZY VERSION OF THIS CLASS, NO METHODS SHOULD DIRECTLY
 ACCESS THIS VARIABLE.

NULL_ALLELE - Static variable in class htsjdk.variant.vcf.VCFConstants
 
NULL_QUALS - Static variable in class htsjdk.samtools.SAMRecord

This should rarely be used, since all reads should have quality scores.

NULL_QUALS_STRING - Static variable in class htsjdk.samtools.SAMRecord
 
NULL_SEQUENCE - Static variable in class htsjdk.samtools.SAMRecord

This should rarely be used, since a read with no sequence doesn't make much sense.

NULL_SEQUENCE_STRING - Static variable in class htsjdk.samtools.SAMRecord
 
NullEncoding<T> - Class in htsjdk.samtools.cram.encoding
 
NullEncoding() - Constructor for class htsjdk.samtools.cram.encoding.NullEncoding
 
NUM_STANDARD_FIELDS - Static variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
numberOfBits(T) - Method in class htsjdk.samtools.cram.encoding.AbstractBitCodec
 
numberOfBits(T) - Method in interface htsjdk.samtools.cram.encoding.BitCodec

Calculate the number of bits that the object would take in bit serialized form.

numberOfBits(byte[]) - Method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding.ByteArrayStopCodec
 
numberOfNonNullBins - Variable in class htsjdk.samtools.BinningIndexContent.BinList
 
numberOfReadFeaturesCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
numberOfReadFeaturesCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
numCigarElements() - Method in class htsjdk.samtools.Cigar
 
numDataValues() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
 
numDuplicates() - Method in class htsjdk.samtools.DuplicateSet

Returns the number of duplicates in this set, including the representative record.

numElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Flag
 
numElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
numElements(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
numElements(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
numElements(VariantContext, Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

A convenience access for the number of elements.

numElements(VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.FTGenotypesWriter
 
numElements(VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
 
numElements(VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
 
numElementsFromValue(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
 
numElementsFromValue(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

Given a value, return the number of elements we will encode for it.

numElementsFromValue(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
 
numHeaderLinesToSkip - Variable in class htsjdk.tribble.index.tabix.TabixFormat

This is part of the index header, but does not appear to be used.

numLikelihoods(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods

Compute how many likelihood elements are associated with the given number of alleles
 Equivalent to asking in how many ways N non-negative integers can add up to P is S(N,P)
 where P = ploidy (number of chromosomes) and N = total # of alleles.





O

OBJECT_TOSTRING_COMPARATOR - Static variable in class htsjdk.samtools.util.CollectionUtil

Simple case-insensitive lexical comparator of objects using their Object.toString() value.

obtainAssertedMate(Iterator<SAMRecord>, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil

Obtain the secondOfPair mate belonging to the firstOfPair SAMRecord
 (assumed to be in the next element of the specified samRecordIterator)

OC - Static variable in class htsjdk.samtools.ReservedTagConstants

The original cigar before indel cleaning, or 454 cafie and homopolymer correction

of(String) - Static method in enum htsjdk.samtools.SamFlagField

Returns the type of flag field for this string.

of(File) - Static method in class htsjdk.samtools.SamInputResource

Creates a SamInputResource reading from the provided resource, with no index.

of(Path) - Static method in class htsjdk.samtools.SamInputResource

Creates a SamInputResource reading from the provided resource, with no index.

of(InputStream) - Static method in class htsjdk.samtools.SamInputResource

Creates a SamInputResource reading from the provided resource, with no index.

of(URL) - Static method in class htsjdk.samtools.SamInputResource

Creates a SamInputResource reading from the provided resource, with no index.

of(SeekableStream) - Static method in class htsjdk.samtools.SamInputResource

Creates a SamInputResource reading from the provided resource, with no index.

of(SRAAccession) - Static method in class htsjdk.samtools.SamInputResource
 
of(String) - Static method in class htsjdk.samtools.SamInputResource

Creates a SamInputResource from a string specifying *either* a url or a file path

offer(E) - Method in class htsjdk.samtools.util.DiskBackedQueue
 
offset - Variable in class htsjdk.samtools.cram.structure.Container

Container start in the stream.

offset - Variable in class htsjdk.samtools.cram.structure.Slice
 
offset - Variable in class htsjdk.samtools.util.AbstractRecordAndOffset

Zero-based offset in the read corresponding to the current position in AbstractLocusInfo

OLD_DEPTH_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
ONE_GB - Static variable in class htsjdk.samtools.util.IOUtil
 
oneAllele(String, List<Allele>) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec

create a an allele from an index and an array of alleles

oneIsPrefixOfOther(Allele, Allele) - Static method in class htsjdk.variant.variantcontext.Allele
 
open(URL) - Method in interface htsjdk.samtools.CustomReaderFactory.ICustomReaderFactory
 
open(File) - Method in class htsjdk.samtools.SamReaderFactory
 
open(Path) - Method in class htsjdk.samtools.SamReaderFactory
 
open(SamInputResource) - Method in class htsjdk.samtools.SamReaderFactory
 
openCraiFileAsBaiStream(File, SAMSequenceDictionary) - Static method in class htsjdk.samtools.cram.CRAIIndex
 
openCraiFileAsBaiStream(InputStream, SAMSequenceDictionary) - Static method in class htsjdk.samtools.cram.CRAIIndex
 
openFileForBufferedReading(File) - Static method in class htsjdk.samtools.util.IOUtil

Checks that a file exists and is readable, and then returns a buffered reader for it.

openFileForBufferedUtf8Reading(File) - Static method in class htsjdk.samtools.util.IOUtil

Opens a file for reading, decompressing it if necessary

openFileForBufferedUtf8Writing(File) - Static method in class htsjdk.samtools.util.IOUtil

Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error

openFileForBufferedWriting(File, boolean) - Static method in class htsjdk.samtools.util.IOUtil

Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error

openFileForBufferedWriting(File) - Static method in class htsjdk.samtools.util.IOUtil

Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error

openFileForMd5CalculatingWriting(File) - Static method in class htsjdk.samtools.util.IOUtil
 
openFileForReading(File) - Static method in class htsjdk.samtools.util.IOUtil

Opens a file for reading, decompressing it if necessary

openFileForReading(Path) - Static method in class htsjdk.samtools.util.IOUtil

Opens a file for reading, decompressing it if necessary

openFileForWriting(File) - Static method in class htsjdk.samtools.util.IOUtil

Opens a file for writing, overwriting the file if it already exists

openFileForWriting(File, boolean) - Static method in class htsjdk.samtools.util.IOUtil

Opens a file for writing

openGzipFileForReading(File) - Static method in class htsjdk.samtools.util.IOUtil

Opens a GZIP-encoded file for reading, decompressing it if necessary

openGzipFileForReading(Path) - Static method in class htsjdk.samtools.util.IOUtil

Opens a GZIP-encoded file for reading, decompressing it if necessary

openGzipFileForWriting(File, boolean) - Static method in class htsjdk.samtools.util.IOUtil

Opens a GZIP encoded file for writing

openIndexFileAsBaiOrNull(File, SAMSequenceDictionary) - Static method in enum htsjdk.samtools.SamIndexes
 
openIndexUrlAsBaiOrNull(URL, SAMSequenceDictionary) - Static method in enum htsjdk.samtools.SamIndexes
 
openInputStream() - Method in class htsjdk.tribble.util.FTPHelper
 
openInputStream() - Method in class htsjdk.tribble.util.HTTPHelper
 
openInputStream(String) - Static method in class htsjdk.tribble.util.ParsingUtils
 
openInputStream() - Method in class htsjdk.tribble.util.RemoteURLHelper
 
openInputStream() - Method in interface htsjdk.tribble.util.URLHelper
 
openInputStreamForRange(long, long) - Method in class htsjdk.tribble.util.FTPHelper

Deprecated.

openInputStreamForRange(long, long) - Method in class htsjdk.tribble.util.HTTPHelper

Deprecated.

openInputStreamForRange(long, long) - Method in class htsjdk.tribble.util.RemoteURLHelper

Deprecated.

openInputStreamForRange(long, long) - Method in interface htsjdk.tribble.util.URLHelper

Deprecated.
Will be removed in a future release, as is somewhat fragile
 and not used.


openOutputStream(File) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.
Returns a output stream writing to location, or throws an exception if this fails

openSamExamples() - Method in class htsjdk.samtools.example.ExampleSamUsage

Example usages of SamReaderFactory

operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Bases
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
optimize(double) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
optimize(double) - Method in class htsjdk.tribble.index.linear.LinearIndex

Adapative optimization of the linear index

optimize() - Method in class htsjdk.tribble.index.linear.LinearIndex
 
optimizeChunkList(List<Chunk>, long) - Method in class htsjdk.samtools.AbstractBAMFileIndex

Deprecated.
Invoke Chunk.optimizeChunkList(java.util.List<htsjdk.samtools.Chunk>, long) directly.


optimizeChunkList(List<Chunk>, long) - Static method in class htsjdk.samtools.Chunk
 
optimizeIntervals(QueryInterval[]) - Static method in class htsjdk.samtools.QueryInterval
 
Options - Enum in htsjdk.variant.variantcontext.writer

Available writer options for VariantContextWriters

options - Variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
 
OQ - Static variable in class htsjdk.samtools.ReservedTagConstants

The original pred quality scores before modifications such as 454 cafie and homopolymer correction

OQ - Variable in class htsjdk.samtools.SAMTagUtil
 
OverclippedReadFilter - Class in htsjdk.samtools.filter

Filters out reads with very few unclipped bases, likely due to the read coming
 from a foreign organism, e.g.

OverclippedReadFilter(int, boolean) - Constructor for class htsjdk.samtools.filter.OverclippedReadFilter
 
OVERFLOW_ELEMENT_MARKER - Static variable in class htsjdk.variant.bcf2.BCF2Utils
 
OverlapDetector<T> - Class in htsjdk.samtools.util

Utility class to efficiently do in memory overlap detection between a large
 set of mapping like objects, and one or more candidate mappings.

OverlapDetector(int, int) - Constructor for class htsjdk.samtools.util.OverlapDetector

Constructs an overlap detector.

OverlapIterator(int, int) - Constructor for class htsjdk.samtools.util.IntervalTree.OverlapIterator
 
overlappers(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Return an iterator over all intervals overlapping the specified range.

overlaps(Chunk) - Method in class htsjdk.samtools.Chunk

Returns whether two chunks overlap.

overlaps(QueryInterval) - Method in class htsjdk.samtools.QueryInterval
 
overlaps(int, int, int, int) - Static method in class htsjdk.samtools.util.CoordMath

Checks to see if the two sets of coordinates have any overlap.

overlaps(Interval) - Method in class htsjdk.tribble.index.interval.Interval
 
overlapsAny(Locatable) - Method in class htsjdk.samtools.util.OverlapDetector

Returns true iff the given locatable overlaps any locatable in this detector.





P

pad(int, int) - Method in class htsjdk.samtools.util.Interval

Returns a new interval that is padded by the amount of bases specified on either side.

padded(int, int) - Method in class htsjdk.samtools.util.IntervalList

Returns a new IntervalList where each interval is padded by the specified amount of bases.

padded(int) - Method in class htsjdk.samtools.util.IntervalList

Returns a new IntervalList where each interval is padded by 'padding' bases on each side.

PADDING - Static variable in enum htsjdk.samtools.CigarOperator
 
Padding - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing padding, similar to CigarOperator.P.

Padding() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
Padding(int, int) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
paddingCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
paddingCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
param - Variable in class htsjdk.samtools.cram.lossy.BaseCategory
 
param - Variable in class htsjdk.samtools.cram.lossy.QualityScoreTreatment
 
param - Variable in class htsjdk.samtools.cram.lossy.ReadCategory
 
params - Variable in class htsjdk.samtools.cram.structure.EncodingParams
 
parse(String) - Method in interface htsjdk.samtools.metrics.Header

Parses the data contained in the String version of the header.

parse(String) - Method in class htsjdk.samtools.metrics.StringHeader
 
parse(String) - Method in class htsjdk.samtools.metrics.VersionHeader
 
parse(String) - Method in enum htsjdk.samtools.SamFlagField

Parses the flag.

parse(String) - Static method in class htsjdk.samtools.util.DateParser

Parse the given string in ISO 8601 format and build a Date object.

parse(Object) - Method in class htsjdk.variant.bcf2.BCF2LazyGenotypesDecoder
 
parse(Object) - Method in interface htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser
 
parseAlleles(String, String, int) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec

parse out the alleles

parseBoolean(String) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into a boolean, as per the above convention that true = Y and false = N.

parseChar(String) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into a char.

parseColor(String) - Static method in class htsjdk.tribble.util.ParsingUtils

Convert an rgb string, hex, or symbol to a color.

parseDate(String) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into a date.

parseDefault(String) - Static method in enum htsjdk.samtools.SamFlagField

Infers the format from the flag string and parses the flag.

parseDouble(String) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into a double.

parseEnum(String, Class<E>) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into an Enum of the given type.

parseFilters(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec

parse the filter string, first checking to see if we already have parsed it in a previous attempt

parseFilters(String) - Method in class htsjdk.variant.vcf.VCF3Codec

parse the filter string, first checking to see if we already have parsed it in a previous attempt

parseFilters(String) - Method in class htsjdk.variant.vcf.VCFCodec

parse the filter string, first checking to see if we already have parsed it in a previous attempt

parseFloat(String) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into a float.

parseGenotypeAlleles(String, List<Allele>, Map<String, List<Allele>>) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec

parse genotype alleles from the genotype string

parseHeaderFromLines(List<String>, VCFHeaderVersion) - Method in class htsjdk.variant.vcf.AbstractVCFCodec

create a VCF header from a set of header record lines

parseInt(String) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into an int.

parseIso8601Date(String) - Method in class htsjdk.samtools.util.FormatUtil

Parse a String into an Iso8601 Date

parseLine(String) - Method in class htsjdk.samtools.SAMLineParser

Parse a SAM line.

parseLine(String, int) - Method in class htsjdk.samtools.SAMLineParser

Parse a SAM line.

parseLine(VCFHeaderVersion, String, List<String>) - Static method in class htsjdk.variant.vcf.VCFHeaderLineTranslator
 
parseLong(String) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into a long.

parseObject(String, Class<?>) - Method in class htsjdk.samtools.util.FormatUtil

Attempts to determine the correct parse method to call based on the desired
 return type and then parses the String and returns the value.

parseQual(String) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec

parse out the qual value

parseReg(String) - Method in class htsjdk.tribble.readers.TabixReader

Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"

parseShort(String) - Method in class htsjdk.samtools.util.FormatUtil

Parses a String into a short.

parseTime - Variable in class htsjdk.samtools.cram.structure.Container
 
parseWithoutValidation(String) - Method in enum htsjdk.samtools.SamFlagField

Performs the actual parsing based on the radix.

ParsingUtils - Class in htsjdk.tribble.util
 
ParsingUtils() - Constructor for class htsjdk.tribble.util.ParsingUtils
 
partition(Collection<V>, CollectionUtil.Partitioner<V, K>) - Static method in class htsjdk.samtools.util.CollectionUtil

Deprecated.
use java8 .stream().collect(Collectors.groupingBy(()-> function)) instead


partition(Collection<V>, Function<? super V, ? extends K>) - Static method in class htsjdk.samtools.util.CollectionUtil

Partitions a collection into groups based on a characteristics of that group.

Partitioner() - Constructor for class htsjdk.samtools.util.CollectionUtil.Partitioner

Deprecated.
 
parts - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
PASSES_FILTERS - Static variable in class htsjdk.variant.variantcontext.VariantContext
 
PASSES_FILTERS_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
PASSES_FILTERS_v4 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
passFilters() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells this builder that the resulting VariantContext should have PASS filters

PassingVariantFilter - Class in htsjdk.variant.variantcontext.filter

A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).

PassingVariantFilter() - Constructor for class htsjdk.variant.variantcontext.filter.PassingVariantFilter
 
pasv() - Method in class htsjdk.samtools.util.ftp.FTPClient
 
peek() - Method in class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
 
peek() - Method in class htsjdk.samtools.util.AbstractIterator

Returns the next element in the iterator, if one exists.

peek() - Method in class htsjdk.samtools.util.BufferedLineReader

Non-destructive one-character look-ahead.

peek() - Method in class htsjdk.samtools.util.DiskBackedQueue
 
peek() - Method in interface htsjdk.samtools.util.LineReader

Non-destructive one-character look-ahead.

peek() - Method in class htsjdk.samtools.util.PeekableIterator

Returns the next object but does not advance the iterator.

peek() - Method in class htsjdk.samtools.util.PeekIterator
 
peek() - Method in class htsjdk.samtools.util.StringLineReader

Non-destructive one-character look-ahead.

peek() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
 
peek() - Method in interface htsjdk.tribble.readers.LineIterator

Peeks at the next line, without expending any elements in the underlying iterator.

peek() - Method in interface htsjdk.tribble.readers.Positional

Return the next byte in the first, without actually reading it from the stream.

peek() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
 
PeekableIterator<Object> - Class in htsjdk.samtools.util

Generic Closable Iterator that allows you to peek at the next value before calling next

PeekableIterator(Iterator<Object>) - Constructor for class htsjdk.samtools.util.PeekableIterator

Constructs a new iterator that wraps the supplied iterator.

peekByte() - Method in class htsjdk.samtools.util.FastLineReader
 
PeekIterator<T> - Class in htsjdk.samtools.util

Wrapper around an iterator that enables non-destructive peeking at the next element that would
 be returned by next()

PeekIterator(Iterator<T>) - Constructor for class htsjdk.samtools.util.PeekIterator
 
PER_ALLELE_COUNT - Static variable in class htsjdk.variant.vcf.VCFConstants
 
PER_ALTERNATE_COUNT - Static variable in class htsjdk.variant.vcf.VCFConstants
 
PER_GENOTYPE_COUNT - Static variable in class htsjdk.variant.vcf.VCFConstants
 
PG - Variable in class htsjdk.samtools.SAMTagUtil
 
PgIdGenerator(SAMFileHeader) - Constructor for class htsjdk.samtools.SAMFileHeader.PgIdGenerator
 
PHASE_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
PHASE_SET_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
phased(boolean) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Is this genotype phased?

PHASED - Static variable in class htsjdk.variant.vcf.VCFConstants
 
PHASED_ALLELE_SEPARATOR - Static variable in class htsjdk.variant.variantcontext.Genotype
 
PHASED_SWITCH_PROB_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
PHASING_TOKENS - Static variable in class htsjdk.variant.vcf.VCFConstants
 
PHRED_ADDEND - Static variable in class htsjdk.samtools.util.SolexaQualityConverter

This value is added to a Phred scord to make it printable ASCII

phredToFastq(byte[]) - Static method in class htsjdk.samtools.SAMUtils

Convert an array of bytes, in which each byte is a binary phred quality score, to
 printable ASCII representation of the quality scores, ala FASTQ format.

phredToFastq(byte[], int, int) - Static method in class htsjdk.samtools.SAMUtils

Convert an array of bytes, in which each byte is a binary phred quality score, to
 printable ASCII representation of the quality scores, ala FASTQ format.

phredToFastq(int) - Static method in class htsjdk.samtools.SAMUtils

Convert a single binary phred score to printable ASCII representation, ala FASTQ format.

pileup(int) - Static method in class htsjdk.samtools.cram.lossy.BaseCategory
 
PL(int[]) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

This genotype has this PL value, as int[].

PL(double[]) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

This genotype has this PL value, converted from double[].

PLAccessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.PLAccessor
 
PLATFORM_MODEL_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
PLATFORM_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
PLATFORM_UNIT_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
PLindexConversion - Static variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
poll() - Method in class htsjdk.samtools.util.DiskBackedQueue
 
position() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
 
position() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
position() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
position() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
position() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
 
position() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
position() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
 
position() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
 
position() - Method in class htsjdk.samtools.seekablestream.SeekableStream
 
Positional - Interface in htsjdk.tribble.readers

Minimal interface for an object at support getting the current position in the stream / writer / file, as well as a handful of other
 reader-like features.

PositionalBufferedStream - Class in htsjdk.tribble.readers

A wrapper around an InputStream which performs it's own buffering, and keeps track of the position.

PositionalBufferedStream(InputStream) - Constructor for class htsjdk.tribble.readers.PositionalBufferedStream
 
PositionalBufferedStream(InputStream, int) - Constructor for class htsjdk.tribble.readers.PositionalBufferedStream
 
PositionalOutputStream - Class in htsjdk.samtools.util

Wraps output stream in a manner which keeps track of the position within the file and allowing writes
 at arbitrary points

PositionalOutputStream(OutputStream) - Constructor for class htsjdk.samtools.util.PositionalOutputStream
 
positiveFourDigitBase36Str(int) - Static method in class htsjdk.samtools.SamFileHeaderMerger

Convert an integer to base36, protected solely for testing

PQ - Variable in class htsjdk.samtools.SAMTagUtil
 
PREDICTED_MEDIAN_INSERT_SIZE_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
prefillBins(K...) - Method in class htsjdk.samtools.util.Histogram

Prefill the histogram with the supplied set of bins.

PREMATURE_END_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
 
PreservationPolicy - Class in htsjdk.samtools.cram.lossy
 
PreservationPolicy() - Constructor for class htsjdk.samtools.cram.lossy.PreservationPolicy
 
preserve() - Static method in class htsjdk.samtools.cram.lossy.QualityScoreTreatment
 
preserveReadNames - Variable in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
previous - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
PREVIOUS_PROGRAM_GROUP_ID_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
 
PRIMARY_KEYS - Static variable in class htsjdk.variant.variantcontext.Genotype

A list of genotype field keys corresponding to values we
 manage inline in the Genotype object.

PrimitiveSamReaderToSamReaderAdapter(SamReader.PrimitiveSamReader, SamInputResource) - Constructor for class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
printHeaderFields(URL) - Static method in class htsjdk.samtools.util.HttpUtils
 
printIndexInfo() - Method in class htsjdk.tribble.index.AbstractIndex
 
printIndexStats(File) - Static method in class htsjdk.samtools.BAMIndexMetaData

Prints meta-data statistics from BAM index (.bai) file
 Statistics include count of aligned and unaligned reads for each reference sequence
 and a count of all records with no start coordinate

printNode() - Method in class htsjdk.samtools.util.IntervalTree.Node
 
PrintReadsExample - Class in htsjdk.samtools.example

This is a example program showing how to use SAM readers and (optionally) writers.

printTree() - Method in class htsjdk.samtools.util.IntervalTree

This method draws a nested picture of the tree on System.out.

printTree() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
 
printTree() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
 
printUsage() - Static method in class htsjdk.tribble.example.CountRecords

print usage information

printUsage() - Static method in class htsjdk.tribble.example.IndexToTable

print usage information

printUsage() - Static method in class htsjdk.tribble.example.IndicesAreEqual

print usage information

printUsage() - Static method in class htsjdk.tribble.example.ProfileIndexReading

print usage information

PrintVariantsExample - Class in htsjdk.variant.example

This is a example program showing how to use Feature readers and (optionally) writers.

processAlignment(SAMRecord) - Method in class htsjdk.samtools.BAMIndexer

Record any index information for a given BAM record.

processContainer(Container) - Method in class htsjdk.samtools.cram.CRAIIndex

Create index entries for a single container.

processContainer(Container, ValidationStringency) - Method in class htsjdk.samtools.CRAMBAIIndexer

Index a container, any of mapped, unmapped and multiple references are allowed.

processContainer(Container) - Method in class htsjdk.samtools.CRAMCRAIIndexer

Create index entries for a single container.

ProcessExecutor - Class in htsjdk.samtools.util

Utility class that will execute sub processes via Runtime.getRuntime().exec(...) and read
 off the output from stderr and stdout of the sub process.

ProcessExecutor() - Constructor for class htsjdk.samtools.util.ProcessExecutor
 
ProcessExecutor.ExitStatusAndOutput - Class in htsjdk.samtools.util
 
processFeature(BinningIndexBuilder.FeatureToBeIndexed) - Method in class htsjdk.samtools.BinningIndexBuilder
 
processSingleReferenceSlice(Slice) - Method in class htsjdk.samtools.CRAMBAIIndexer

Record index information for a given CRAM slice that contains either unmapped reads or
 reads mapped to a single reference.

processValidationError(SAMValidationError, ValidationStringency) - Static method in class htsjdk.samtools.SAMUtils
 
processValidationErrors(List<SAMValidationError>, long, ValidationStringency) - Static method in class htsjdk.samtools.SAMUtils

Handle a list of validation errors according to the validation stringency.

ProfileIndexReading - Class in htsjdk.tribble.example
 
ProfileIndexReading() - Constructor for class htsjdk.tribble.example.ProfileIndexReading
 
PROGRAM_GROUP_ID - Static variable in class htsjdk.samtools.ReservedTagConstants
 
PROGRAM_GROUP_ID_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
 
PROGRAM_GROUP_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
PROGRAM_NAME_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
 
PROGRAM_VERSION_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
 
ProgressLogger - Class in htsjdk.samtools.util

Little progress logging class to facilitate consistent output of useful information when progressing
 through a stream of SAM records.

ProgressLogger(Log, int, String, String) - Constructor for class htsjdk.samtools.util.ProgressLogger

Construct a progress logger.

ProgressLogger(Log, int, String) - Constructor for class htsjdk.samtools.util.ProgressLogger

Construct a progress logger.

ProgressLogger(Log, int) - Constructor for class htsjdk.samtools.util.ProgressLogger

Construct a progress logger with the desired log and frequency and the verb "Processed".

ProgressLogger(Log) - Constructor for class htsjdk.samtools.util.ProgressLogger

Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.

ProgressLoggerInterface - Interface in htsjdk.samtools.util

An interface defining the record() methods of the Picard-public ProgressLogger implementation.

PROPER_PAIR_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
properties - Variable in class htsjdk.tribble.index.TribbleIndexCreator
 
PSLTBL - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
 
PU - Variable in class htsjdk.samtools.SAMTagUtil
 
push(double) - Method in class htsjdk.tribble.util.MathUtils.RunningStat
 
put(int, KEY, REC) - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap

Store the record with the given sequence index and key.

put(int, T) - Method in class htsjdk.samtools.cram.common.IntHashMap


 Maps the specified key to the specified value
 in this hashtable.

put(int, int, V) - Method in class htsjdk.samtools.util.IntervalTree

Put a new interval into the tree (or update the value associated with an existing interval).

put(Interval, T) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
putAttribute(String, Object) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
putAttribute(String, Object, boolean) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
putAttributes(Map<String, ?>) - Method in class htsjdk.variant.variantcontext.CommonInfo
 




Q

Q2 - Variable in class htsjdk.samtools.SAMTagUtil
 
QUALITY_HEADER - Static variable in class htsjdk.samtools.fastq.FastqConstants
 
QualityEncodingDetector - Class in htsjdk.samtools.util

Utility for determining the type of quality encoding/format (see FastqQualityFormat) used in a SAM/BAM or Fastq.

QualityEncodingDetector() - Constructor for class htsjdk.samtools.util.QualityEncodingDetector
 
QualityEncodingDetector.FileContext - Enum in htsjdk.samtools.util
 
qualityScoreArrayCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
qualityScoreCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
qualityScoreCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
QualityScorePreservation - Class in htsjdk.samtools.cram.lossy
 
QualityScorePreservation(String) - Constructor for class htsjdk.samtools.cram.lossy.QualityScorePreservation
 
qualityScores - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
qualityScoresCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
QualityScoreTreatment - Class in htsjdk.samtools.cram.lossy
 
QualityScoreTreatmentType - Enum in htsjdk.samtools.cram.lossy
 
QualityUtil - Class in htsjdk.samtools.util

Utility class for working with quality scores and error probabilities.

QualityUtil() - Constructor for class htsjdk.samtools.util.QualityUtil
 
query(int, int, int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
 
query(QueryInterval[], boolean) - Method in class htsjdk.samtools.CRAMFileReader
 
query(QueryInterval[], boolean) - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
query(QueryInterval[], boolean) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
query(String, int, int, boolean) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
query(String, int, int, boolean) - Method in interface htsjdk.samtools.SamReader

Iterate over records that match the given interval.

query(QueryInterval[], boolean) - Method in interface htsjdk.samtools.SamReader

Iterate over records that match one of the given intervals.

query(QueryInterval[], boolean) - Method in class htsjdk.samtools.SRAFileReader
 
query(String, int, int) - Method in interface htsjdk.tribble.FeatureReader
 
query(int, int, int) - Method in class htsjdk.tribble.readers.TabixReader

Return

query(String) - Method in class htsjdk.tribble.readers.TabixReader
 
query(String, int, int) - Method in class htsjdk.tribble.readers.TabixReader
 
query(String, int, int) - Method in class htsjdk.tribble.TabixFeatureReader

Return iterator over all features overlapping the given interval

query(String, int, int) - Method in class htsjdk.tribble.TribbleIndexedFeatureReader

Return an iterator to iterate over features overlapping the specified interval
 
 Note that TribbleIndexedFeatureReader only supports issuing and manipulating a single query
 for each reader.

query(String, int, int) - Method in class htsjdk.variant.vcf.VCFFileReader

Queries for records within the region specified.

queryAlignmentStart(String, int) - Method in class htsjdk.samtools.CRAMFileReader
 
queryAlignmentStart(String, int) - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
queryAlignmentStart(String, int) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
queryAlignmentStart(String, int) - Method in interface htsjdk.samtools.SamReader

Iterate over records that map to the given sequence and start at the given position.

queryAlignmentStart(String, int) - Method in class htsjdk.samtools.SRAFileReader
 
queryContained(String, int, int) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
queryContained(QueryInterval[]) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
queryContained(String, int, int) - Method in interface htsjdk.samtools.SamReader

Iterate over records that are contained in the given interval.

queryContained(QueryInterval[]) - Method in interface htsjdk.samtools.SamReader

Iterate over records that are contained in the given interval.

QueryInterval - Class in htsjdk.samtools

Interval relative to a reference, for querying a BAM file.

QueryInterval(int, int, int) - Constructor for class htsjdk.samtools.QueryInterval
 
queryMate(SAMRecord) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter

Wraps the boilerplate code for querying a record's mate, which is common across many implementations.

queryMate(SAMRecord) - Method in interface htsjdk.samtools.SamReader

Fetch the mate for the given read.

queryOverlapping(String, int, int) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
queryOverlapping(QueryInterval[]) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
queryOverlapping(String, int, int) - Method in interface htsjdk.samtools.SamReader

Iterate over records that overlap the given interval.

queryOverlapping(QueryInterval[]) - Method in interface htsjdk.samtools.SamReader

Iterate over records that overlap any of the given intervals.

queryUnmapped() - Method in class htsjdk.samtools.CRAMFileReader
 
queryUnmapped() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
queryUnmapped() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
queryUnmapped() - Method in interface htsjdk.samtools.SamReader
 
queryUnmapped() - Method in class htsjdk.samtools.SRAFileReader
 
quit() - Method in class htsjdk.samtools.util.ftp.FTPClient
 




R

R2 - Variable in class htsjdk.samtools.SAMTagUtil
 
RANS - Class in htsjdk.samtools.cram.encoding.rans
 
RANS() - Constructor for class htsjdk.samtools.cram.encoding.rans.RANS
 
rans(byte[], RANS.ORDER) - Static method in class htsjdk.samtools.cram.io.ExternalCompression

Compress a byte array into rANS blob.

rans(byte[], int) - Static method in class htsjdk.samtools.cram.io.ExternalCompression

Compress a byte array into rANS blob.

RANS.ORDER - Enum in htsjdk.samtools.cram.encoding.rans
 
read(BitInputStream) - Method in class htsjdk.samtools.cram.encoding.AbstractBitCodec
 
read(BitInputStream, int) - Method in class htsjdk.samtools.cram.encoding.AbstractBitCodec
 
read(BitInputStream) - Method in interface htsjdk.samtools.cram.encoding.BitCodec

Read a single object from the bit stream.

read(BitInputStream, int) - Method in interface htsjdk.samtools.cram.encoding.BitCodec

Read a array of specified length from the bit stream.

read(BitInputStream) - Method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding.ByteArrayStopCodec
 
read(BitInputStream, int) - Method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding.ByteArrayStopCodec
 
read(CramCompressionRecord) - Method in class htsjdk.samtools.cram.encoding.reader.CramRecordReader
 
read() - Method in class htsjdk.samtools.cram.encoding.reader.RefSeqIdReader
 
read() - Method in class htsjdk.samtools.cram.io.CountingInputStream
 
read(byte[]) - Method in class htsjdk.samtools.cram.io.CountingInputStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.cram.io.CountingInputStream
 
read() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
 
read(byte[]) - Method in class htsjdk.samtools.cram.io.CRC32InputStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.cram.io.CRC32InputStream
 
read(byte[]) - Method in class htsjdk.samtools.cram.structure.CompressionHeader
 
read(Reader) - Method in class htsjdk.samtools.metrics.MetricsFile

Reads the Metrics in from the given reader.

read() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
 
read() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
read() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
read(byte[]) - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
read() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
 
read() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
read() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
 
read() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
 
read() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableStream
 
read() - Method in class htsjdk.samtools.util.BlockCompressedInputStream

Reads the next byte of data from the input stream.

read(byte[]) - Method in class htsjdk.samtools.util.BlockCompressedInputStream

Reads some number of bytes from the input stream and stores them into the buffer array b.

read(byte[], int, int) - Method in class htsjdk.samtools.util.BlockCompressedInputStream

Reads up to len bytes of data from the input stream into an array of bytes.

read() - Method in class htsjdk.samtools.util.CoordSpanInputSteam
 
read(byte[], int, int) - Method in class htsjdk.samtools.util.CoordSpanInputSteam
 
read(byte[], int, int) - Method in class htsjdk.samtools.util.ftp.FTPStream
 
read() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
 
read(byte[]) - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
 
read(byte[], int, int) - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
 
read(LittleEndianInputStream) - Method in class htsjdk.tribble.index.AbstractIndex
 
read(LittleEndianInputStream) - Method in interface htsjdk.tribble.index.ChrIndex
 
read(LittleEndianInputStream) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
 
read(LittleEndianInputStream) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
read() - Method in class htsjdk.tribble.readers.LongLineBufferedReader

Reads a single character.

read(char[], int, int) - Method in class htsjdk.tribble.readers.LongLineBufferedReader

Reads characters into a portion of an array.

read() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
 
read(byte[], int, int) - Method in class htsjdk.tribble.readers.PositionalBufferedStream
 
read(byte[]) - Method in class htsjdk.tribble.readers.PositionalBufferedStream
 
read(InputStream) - Method in enum htsjdk.variant.bcf2.BCF2Type

Read a value from in stream of this BCF2 type as an int [32 bit] collection of bits

 For intX and char values this is just the int / byte value of the underlying data represented as a 32 bit int
 For a char the result must be converted to a char by (char)(byte)(0x0F & value)
 For doubles it's necessary to convert subsequently this value to a double via Double.bitsToDouble()

READ_FAILS_VENDOR_QUALITY_CHECK_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
READ_GROUP_ID - Static variable in class htsjdk.samtools.ReservedTagConstants
 
READ_GROUP_ID_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
READ_GROUP_SAMPLE_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
READ_PAIRED_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
READ_STRAND_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
READ_TIMEOUT - Static variable in class htsjdk.samtools.util.ftp.FTPClient
 
READ_UNMAPPED_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
readActualHeader(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec

Read and return the header, or null if there is no header.

readActualHeader(LineIterator) - Method in class htsjdk.tribble.bed.BEDCodec
 
readActualHeader(LineIterator) - Method in class htsjdk.tribble.gelitext.GeliTextCodec

Deprecated.
 
readActualHeader(LineIterator) - Method in class htsjdk.variant.vcf.VCF3Codec
 
readActualHeader(LineIterator) - Method in class htsjdk.variant.vcf.VCFCodec

Reads all of the header from the provided iterator, but no reads no further.

ReadBase - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing a single base with associated quality score.

ReadBase(int, byte, byte) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
readBaseMatchesRefBaseWithAmbiguity(byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil

Efficiently compare two IUPAC base codes, one coming from a read sequence and the other coming from
 a reference sequence, using the reference code as a 'pattern' that the read base must match.

readBases - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
readBCFVersion(InputStream) - Static method in class htsjdk.variant.bcf2.BCFVersion

Return a new BCFVersion object describing the major and minor version of the BCF file in stream

 Note that stream must be at the very start of the file.

readBeans(File) - Static method in class htsjdk.samtools.metrics.MetricsFile

Convenience method to read all the Metric beans from a metrics file.

readBit() - Method in interface htsjdk.samtools.cram.io.BitInputStream

Reads a single bit from the stream.

readBit() - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
 
readBits(int) - Method in interface htsjdk.samtools.cram.io.BitInputStream

Read specified number of bits from the stream.

readBits(int) - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
 
readBlockSize(InputStream) - Method in class htsjdk.variant.bcf2.BCF2Decoder

Read the size of the next block from inputStream

readBoolean() - Method in class htsjdk.samtools.util.BinaryCodec

Reads a boolean off the input stream, represented as a byte with value 1 or 0

readByte() - Method in class htsjdk.samtools.util.BinaryCodec
 
readByte() - Method in class htsjdk.tribble.util.LittleEndianInputStream
 
readByte(InputStream) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
readBytes(byte[]) - Method in class htsjdk.samtools.util.BinaryCodec

Read a byte array from the input stream.

readBytes(byte[], int, int) - Method in class htsjdk.samtools.util.BinaryCodec

Read a byte array from the input stream

readBytesOrFewer(byte[], int, int) - Method in class htsjdk.samtools.util.BinaryCodec

Reads a byte array from the input stream.

readCategory - Variable in class htsjdk.samtools.cram.lossy.PreservationPolicy
 
ReadCategory - Class in htsjdk.samtools.cram.lossy
 
ReadCategoryType - Enum in htsjdk.samtools.cram.lossy
 
readContainer(Version, InputStream) - Static method in class htsjdk.samtools.cram.structure.ContainerIO

Reads a CRAM container from the input stream.

readContainerHeader(int, InputStream) - Static method in class htsjdk.samtools.cram.structure.ContainerIO

Reads container header only from a InputStream.

readCramHeader(InputStream) - Static method in class htsjdk.samtools.cram.build.CramIO

Read CRAM header from the given InputStream.

readData() - Method in interface htsjdk.samtools.cram.encoding.reader.DataReader

Read a single object

readData() - Method in class htsjdk.samtools.cram.encoding.reader.DataReaderFactory.DataReaderWithStats
 
readDataArray(int) - Method in interface htsjdk.samtools.cram.encoding.reader.DataReader

Read an array of specified length.

readDataArray(int) - Method in class htsjdk.samtools.cram.encoding.reader.DataReaderFactory.DataReaderWithStats
 
readDouble() - Method in class htsjdk.samtools.util.BinaryCodec

Reads a double off the input stream

readDouble() - Method in class htsjdk.tribble.util.LittleEndianInputStream
 
ReaderImplementation() - Constructor for class htsjdk.samtools.SamReader.ReaderImplementation
 
ReadFeature - Interface in htsjdk.samtools.cram.encoding.readfeatures

An interface to capture data in read coordinates.

readFeatureCodeCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
readFeaturePositionCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
readFeatures - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
readFloat() - Method in class htsjdk.samtools.util.BinaryCodec

Reads a float off the input stream

readFloat() - Method in class htsjdk.tribble.util.LittleEndianInputStream
 
readFromInputStream(int, InputStream) - Static method in class htsjdk.samtools.cram.structure.Block

Deserialize the block from the InputStream.

readFully(InputStream) - Static method in class htsjdk.samtools.cram.io.InputStreamUtils

Read the InputStream until the end into a new byte array.

readFully(InputStream, int) - Static method in class htsjdk.samtools.cram.io.InputStreamUtils

Read the specified number of bytes from the InputStream into a new byte array.

readFully(InputStream, byte[], int, int) - Static method in class htsjdk.samtools.cram.io.InputStreamUtils

Read the specified number of bytes from the InputStream into the byte array starting from the specified position.

readFully(byte[]) - Method in class htsjdk.samtools.seekablestream.SeekableStream

Read enough bytes to fill the input buffer.

readFully(InputStream) - Static method in class htsjdk.samtools.util.IOUtil

Reads everything from an input stream as characters and returns a single String.

readGroupC - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
readGroupCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
readGroupID - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
readHeader(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec
 
readHeader(PositionalBufferedStream) - Method in class htsjdk.tribble.example.ExampleBinaryCodec
 
readHeader(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec

Read and return the header, or null if there is no header.

readHeader(PositionalBufferedStream) - Method in class htsjdk.variant.bcf2.BCF2Codec
 
readHeaderLine(String) - Method in class htsjdk.tribble.bed.BEDCodec
 
readHeaders(File) - Static method in class htsjdk.samtools.metrics.MetricsFile

Method to read the header from a metrics file.

readIndex(InputStream) - Static method in class htsjdk.samtools.CRAMCRAIIndexer

Read an input stream containing a .crai index and return a CRAIIndex object.

readInt() - Method in class htsjdk.samtools.util.BinaryCodec

Read an int off the input stream

readInt(InputStream) - Static method in class htsjdk.tribble.readers.TabixReader
 
readInt() - Method in class htsjdk.tribble.util.LittleEndianInputStream
 
readInto(BitInputStream, byte[], int, int) - Method in class htsjdk.samtools.cram.encoding.AbstractBitCodec
 
readInto(BitInputStream, byte[], int, int) - Method in interface htsjdk.samtools.cram.encoding.BitCodec

Read a array of specified length from the bit stream into a given byte array.

readLength - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
readLengthAndString(boolean) - Method in class htsjdk.samtools.util.BinaryCodec

Read an int length, and then a String of that length

readLengthC - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
readLengthCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
readLine() - Method in class htsjdk.samtools.util.BlockCompressedInputStream

Reads a whole line.

readLine() - Method in class htsjdk.samtools.util.BufferedLineReader

Read a line and remove the line terminator

readLine() - Method in interface htsjdk.samtools.util.LineReader

Read a line and remove the line terminator

readLine() - Method in class htsjdk.samtools.util.StringLineReader

Read a line and remove the line terminator

readLine(PositionalBufferedStream) - Method in class htsjdk.tribble.readers.AsciiLineReader

Read a line of text.

readLine() - Method in class htsjdk.tribble.readers.AsciiLineReader

Same as AsciiLineReader.readLine(PositionalBufferedStream) but uses the stream provided in the constructor

readLine() - Method in interface htsjdk.tribble.readers.LineReader
 
readLine() - Method in class htsjdk.tribble.readers.LongLineBufferedReader

Reads a line of text.

readLine() - Method in class htsjdk.tribble.readers.SynchronousLineReader
 
readLine() - Method in class htsjdk.tribble.readers.TabixIteratorLineReader
 
readLine(InputStream) - Static method in class htsjdk.tribble.readers.TabixReader
 
readLine() - Method in class htsjdk.tribble.readers.TabixReader

Read one line from the data file.

readLines(File) - Static method in class htsjdk.samtools.util.IOUtil

Returns an iterator over the lines in a text file.

readLong() - Method in class htsjdk.samtools.util.BinaryCodec

Reads a long off the input stream

readLong(InputStream) - Static method in class htsjdk.tribble.readers.TabixReader
 
readLong() - Method in class htsjdk.tribble.util.LittleEndianInputStream
 
readLongBits(int) - Method in interface htsjdk.samtools.cram.io.BitInputStream

Read specified number of bits from the stream.

readLongBits(int) - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
 
readName - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
readNameC - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
readNameCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
ReadNameFilter - Class in htsjdk.samtools.filter

Filter by a set of specified readnames
 
 $Id$

ReadNameFilter(File, boolean) - Constructor for class htsjdk.samtools.filter.ReadNameFilter
 
ReadNameFilter(Set<String>, boolean) - Constructor for class htsjdk.samtools.filter.ReadNameFilter
 
readNamesIncluded - Variable in class htsjdk.samtools.cram.structure.CompressionHeader
 
readNextBlock(int, InputStream) - Method in class htsjdk.variant.bcf2.BCF2Decoder

Reads the next record from input stream and prepare this decoder to decode values from it

readNullTerminatedString() - Method in class htsjdk.samtools.util.BinaryCodec

Read ASCII bytes from the input stream until a null byte is read

readNullTerminatedString(BinaryCodec) - Static method in class htsjdk.samtools.util.StringUtil
 
readShort() - Method in class htsjdk.samtools.util.BinaryCodec
 
readShort() - Method in class htsjdk.tribble.util.LittleEndianInputStream
 
readSingleValue(byte, ByteBuffer, ValidationStringency) - Static method in class htsjdk.samtools.cram.structure.ReadTag
 
readString(int) - Method in class htsjdk.samtools.util.BinaryCodec

Read a string off the input stream, as ASCII bytes

readString() - Method in class htsjdk.tribble.util.LittleEndianInputStream

Read a null terminated byte array and return result as a string

ReadTag - Class in htsjdk.samtools.cram.structure

CRAM counterpart of SAMTag.

ReadTag(int, byte[], ValidationStringency) - Constructor for class htsjdk.samtools.cram.structure.ReadTag
 
readTags(byte[], int, int, ValidationStringency) - Static method in class htsjdk.samtools.BinaryTagCodec

Convert tags from little-endian disk representation to in-memory representation.

readTime - Variable in class htsjdk.samtools.cram.structure.Container
 
readToEndOfOutputBufferOrEoln(byte[], int) - Method in class htsjdk.samtools.util.FastLineReader

Read from input until input is exhausted, EOLN is seen, or output buffer is filled

readTypeDescriptor() - Method in class htsjdk.variant.bcf2.BCF2Decoder
 
readUByte() - Method in class htsjdk.samtools.util.BinaryCodec

Reads an 8-bit unsigned byte from the input stream.

readUInt() - Method in class htsjdk.samtools.util.BinaryCodec

Reads a 32-bit unsigned int from the input stream.

readUnsignedITF8(InputStream) - Static method in class htsjdk.samtools.cram.io.ITF8

Reads an unsigned (32 bit) integer from an InputStream.

readUnsignedITF8(byte[]) - Static method in class htsjdk.samtools.cram.io.ITF8

Reads an unsigned (32 bit) integer from an array of bytes.

readUnsignedITF8(ByteBuffer) - Static method in class htsjdk.samtools.cram.io.ITF8

Reads an unsigned (32 bit) integer from a ByteBuffer.

readUnsignedLTF8(InputStream) - Static method in class htsjdk.samtools.cram.io.LTF8

Reads an unsigned long value from the input stream.

readUShort() - Method in class htsjdk.samtools.util.BinaryCodec

Reads a 16-bit unsigned short from the input stream.

ready() - Method in class htsjdk.tribble.readers.LongLineBufferedReader

Tells whether this stream is ready to be read.

reapplyOptions(SamReader) - Method in class htsjdk.samtools.SamReaderFactory

Reapplies any changed options to the reader *

record(String, int) - Method in class htsjdk.samtools.util.AbstractProgressLogger
 
record(SAMRecord) - Method in class htsjdk.samtools.util.AbstractProgressLogger

Records that a given record has been processed and triggers logging if necessary.

record(SAMRecord...) - Method in class htsjdk.samtools.util.AbstractProgressLogger

Records multiple SAMRecords and triggers logging if necessary.

record - Variable in class htsjdk.samtools.util.AbstractRecordAndOffset

A SAMRecord aligned to reference position

record(String, int) - Method in interface htsjdk.samtools.util.ProgressLoggerInterface
 
record(SAMRecord) - Method in interface htsjdk.samtools.util.ProgressLoggerInterface
 
record(SAMRecord...) - Method in interface htsjdk.samtools.util.ProgressLoggerInterface
 
recordAcceptedRecord() - Method in class htsjdk.samtools.DownsamplingIterator

Method for subclasses to record a specific record as being accepted.

recordAcceptedRecords(long) - Method in class htsjdk.samtools.DownsamplingIterator

Record one or more records as having been discarded.

RecordAndOffset(SAMRecord, int) - Constructor for class htsjdk.samtools.util.SamLocusIterator.RecordAndOffset
 
recordDiscardedRecord() - Method in class htsjdk.samtools.DownsamplingIterator

Method for subclasses to record a record as being discarded.

recordDiscardRecords(long) - Method in class htsjdk.samtools.DownsamplingIterator

Record one or more records as having been discarded.

recordMapsEntirelyBeyondEndOfReference(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils

Tests if the provided record is mapped entirely beyond the end of the reference (i.e., the alignment start is greater than the
 length of the sequence to which the record is mapped).

RecordRangeInfo(List<Long>, long) - Constructor for class htsjdk.samtools.SRAIterator.RecordRangeInfo
 
recordsPerSlice - Variable in class htsjdk.samtools.CRAMContainerStreamWriter
 
recordsToNextFragment - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
recursiveDelete(File) - Static method in class htsjdk.samtools.util.TestUtil

Little test utility to help tests that create multiple levels of subdirectories
 clean up after themselves.

REFERENCE_ALIGNMENT - Static variable in class htsjdk.samtools.sra.SRAUtils

References are stored in SRA table in chunks of 5k bases per row, while last chunk of a reference is less or
 equal than 5k bases in size (even if the next reference follows).

REFERENCE_FASTA - Static variable in class htsjdk.samtools.Defaults

The reference FASTA file.

REFERENCE_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
 
ReferenceCache - Class in htsjdk.samtools.sra

That is a thread-safe wrapper for a list of cache Reference objects.

ReferenceCache(ReadCollection, SAMFileHeader) - Constructor for class htsjdk.samtools.sra.ReferenceCache
 
referenceIndex - Variable in class htsjdk.samtools.QueryInterval

Index of reference sequence, based on the sequence dictionary of the BAM file being queried.

ReferenceSequence - Class in htsjdk.samtools.reference

Wrapper around a reference sequence that has been read from a reference file.

ReferenceSequence(String, int, byte[]) - Constructor for class htsjdk.samtools.reference.ReferenceSequence

creates a fully formed ReferenceSequence

referenceSequence(File) - Method in class htsjdk.samtools.SamReaderFactory

Sets the specified reference sequence *

ReferenceSequenceFile - Interface in htsjdk.samtools.reference

An interface for working with files of reference sequences regardless of the file format
 being used.

ReferenceSequenceFileFactory - Class in htsjdk.samtools.reference

Factory class for creating ReferenceSequenceFile instances for reading reference
 sequences store in various formats.

ReferenceSequenceFileFactory() - Constructor for class htsjdk.samtools.reference.ReferenceSequenceFileFactory
 
ReferenceSequenceFileWalker - Class in htsjdk.samtools.reference

Manages a ReferenceSequenceFile.

ReferenceSequenceFileWalker(ReferenceSequenceFile) - Constructor for class htsjdk.samtools.reference.ReferenceSequenceFileWalker
 
ReferenceSequenceFileWalker(File) - Constructor for class htsjdk.samtools.reference.ReferenceSequenceFileWalker
 
ReferenceSequenceMask - Interface in htsjdk.samtools.util

Interface for specifying loci of interest for genotype calling and other operations.

ReferenceSource - Class in htsjdk.samtools.cram.ref

Used to represent a CRAM reference, the backing source for which can either be
 a file or the EBI ENA reference service.

ReferenceSource(File) - Constructor for class htsjdk.samtools.cram.ref.ReferenceSource
 
ReferenceSource(Path) - Constructor for class htsjdk.samtools.cram.ref.ReferenceSource
 
ReferenceSource(ReferenceSequenceFile) - Constructor for class htsjdk.samtools.cram.ref.ReferenceSource
 
referenceSource() - Method in class htsjdk.samtools.SamReaderFactory
 
referenceSource(CRAMReferenceSource) - Method in class htsjdk.samtools.SamReaderFactory

Sets the specified reference sequence *

ReferenceTracks - Class in htsjdk.samtools.cram.ref
 
ReferenceTracks(int, String, byte[]) - Constructor for class htsjdk.samtools.cram.ref.ReferenceTracks
 
refId - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
refId - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
refIdCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
refIdCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
refMD5 - Variable in class htsjdk.samtools.cram.structure.Slice
 
RefSeqIdReader - Class in htsjdk.samtools.cram.encoding.reader

A reader that only keeps track of alignment spans.

RefSeqIdReader(int, int, ValidationStringency) - Constructor for class htsjdk.samtools.cram.encoding.reader.RefSeqIdReader
 
RefSkip - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing a reference skip similar to CigarOperator.N.

RefSkip() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
RefSkip(int, int) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
refSkipCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
refSkipCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
regionToBin(int, int) - Static method in class htsjdk.samtools.GenomicIndexUtil

calculate the bin given an alignment in [beg,end)
 Described in "The Human Genome Browser at UCSC.

regionToBins(int, int) - Method in class htsjdk.samtools.AbstractBAMFileIndex

Get candidate bins for the specified region

regionToBins(int, int) - Static method in class htsjdk.samtools.GenomicIndexUtil

Get candidate bins for the specified region

registerHelperClass(Class) - Static method in class htsjdk.tribble.util.ParsingUtils

Register a URLHelper class to be used for URL operations.

rehash() - Method in class htsjdk.samtools.cram.common.IntHashMap


 Increases the capacity of and internally reorganizes this hashtable, in
 order to accommodate and access its entries more efficiently.

reheaderBamFile(SAMFileHeader, File, File) - Static method in class htsjdk.samtools.BamFileIoUtils
 
reheaderBamFile(SAMFileHeader, File, File, boolean, boolean) - Static method in class htsjdk.samtools.BamFileIoUtils

Copy a BAM file but replacing the header

RelativeIso8601Date - Class in htsjdk.samtools.util

Like Iso8601Date, but also comes in a "lazy now" flavor.

RelativeIso8601Date(Date) - Constructor for class htsjdk.samtools.util.RelativeIso8601Date
 
RelativeIso8601Date(String) - Constructor for class htsjdk.samtools.util.RelativeIso8601Date
 
remappedSampleName - Variable in class htsjdk.variant.vcf.AbstractVCFCodec

If non-null, we will replace the sample name read from the VCF header with this sample name.

RemoteURLHelper - Class in htsjdk.tribble.util

Implementation of URLHelper designed for remote resources.

RemoteURLHelper(URL) - Constructor for class htsjdk.tribble.util.RemoteURLHelper
 
remove(int, KEY) - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap
 
remove() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
 
remove() - Method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
 
remove(int) - Method in class htsjdk.samtools.cram.common.IntHashMap


 Removes the key (and its corresponding value) from this hashtable.

remove() - Method in class htsjdk.samtools.CRAMIterator
 
remove() - Method in class htsjdk.samtools.DownsamplingIterator

Not supported.

remove() - Method in class htsjdk.samtools.DuplicateSetIterator
 
remove() - Method in class htsjdk.samtools.fastq.FastqReader
 
remove() - Method in class htsjdk.samtools.filter.FilteringSamIterator

Required method for Iterator API.

remove() - Method in class htsjdk.samtools.MergingSamRecordIterator

Unsupported operation.

remove(short) - Method in class htsjdk.samtools.SAMBinaryTagAndValue

Removes a tag from the list and returns the new head of the list/sub-list.

remove() - Method in class htsjdk.samtools.SamReader.AssertingIterator
 
remove() - Method in class htsjdk.samtools.sra.SRAAlignmentIterator
 
remove() - Method in class htsjdk.samtools.sra.SRAUnalignmentIterator
 
remove() - Method in class htsjdk.samtools.SRAIterator
 
remove() - Method in class htsjdk.samtools.util.AbstractIterator
 
remove() - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
remove() - Method in class htsjdk.samtools.util.DelegatingIterator
 
remove() - Method in class htsjdk.samtools.util.DiskBackedQueue
 
remove(Object) - Method in class htsjdk.samtools.util.DiskBackedQueue

Not supported.

remove() - Method in class htsjdk.samtools.util.IntervalTree.FwdIterator
 
remove() - Method in class htsjdk.samtools.util.IntervalTree.OverlapIterator
 
remove(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Remove an interval from the tree.

remove() - Method in class htsjdk.samtools.util.IntervalTree.RevIterator
 
remove() - Method in class htsjdk.samtools.util.IntervalTree.ValuesIterator
 
remove(Object) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
remove(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap
 
remove() - Method in class htsjdk.samtools.util.IterableOnceIterator

Operation not supported.

remove() - Method in class htsjdk.samtools.util.MergingIterator

Unsupported.

remove() - Method in class htsjdk.samtools.util.PeekableIterator

Unsupported Operation.

remove() - Method in class htsjdk.samtools.util.PeekIterator

Unsupported

remove(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap
 
remove() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer

Removes the next record from this buffer

remove() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
 
remove() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator

Required method for Iterator API.

remove(int) - Method in class htsjdk.variant.variantcontext.GenotypesContext

Note that remove requires us to invalidate our sample -> index
 cache.

remove(Object) - Method in class htsjdk.variant.variantcontext.GenotypesContext

See for important warning GenotypesContext.remove(int)

removeAll(Collection<?>) - Method in class htsjdk.samtools.util.DiskBackedQueue

Not supported.

removeAll(Collection<?>) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
removeAttribute(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
removeContentsBefore(SAMFileSpan) - Method in class htsjdk.samtools.BAMFileSpan

Creates a new file span by removing all chunks before the given file span starts.

removeContentsBefore(SAMFileSpan) - Method in interface htsjdk.samtools.SAMFileSpan

Remove all pointers in this file span before the given file span starts.

removeTransientAttribute(Object) - Method in class htsjdk.samtools.SAMRecord

Removes a transient attribute if it is stored, and returns the stored value.

rename(FastaSequenceIndexEntry, String) - Method in class htsjdk.samtools.reference.FastaSequenceIndex

Renames the existing index entry to the new index entry with the specified name.

repairStandardHeaderLines(VCFHeader) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines

Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly
 allocated VCFHeader with standard VCF header lines repaired as necessary.

repeatCharNTimes(char, int) - Static method in class htsjdk.samtools.util.StringUtil
 
replace(Genotype) - Method in class htsjdk.variant.variantcontext.GenotypesContext

Replaces the genotype in this context -- note for efficiency
 reasons we do not add the genotype if it's not present.

replaceCramHeader(File, CramHeader) - Static method in class htsjdk.samtools.cram.build.CramIO

Attempt to replace the SAM file header in the CRAM file.

RESERVED_MRNM_SEQUENCE_NAME - Static variable in class htsjdk.samtools.SAMSequenceRecord

This is not a valid sequence name, because it is reserved in the MRNM field of SAM text format
 to mean "same reference as RNAME field."

ReservedTagConstants - Class in htsjdk.samtools

Constants for tags used in our SAM/BAM files

ReservedTagConstants() - Constructor for class htsjdk.samtools.ReservedTagConstants
 
reset() - Method in class htsjdk.samtools.cram.io.CountingInputStream
 
reset() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
 
reset() - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
 
reset() - Method in class htsjdk.samtools.reference.FastaSequenceFile
 
reset() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile

Reset the iterator over the index.

reset() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile

Resets the ReferenceSequenceFile so that the next call to nextSequence() will return
 the first sequence in the file.

reset() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
reset() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
 
reset() - Method in class htsjdk.samtools.util.StopWatch
 
reset() - Method in class htsjdk.tribble.readers.LongLineBufferedReader

Resets the stream to the most recent mark.

reset(boolean) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

Reset all of the builder attributes to their defaults.

resetStatistics() - Method in class htsjdk.samtools.DownsamplingIterator

Resets the statistics for records seen/accepted/discarded.

resetToDefaultInstance() - Static method in class htsjdk.samtools.CustomReaderFactory
 
resolveIndexFromName(String, SAMFileHeader, boolean) - Static method in class htsjdk.samtools.SAMRecord

Static method that resolves and returns the reference index corresponding to a given reference name.

resolveNameFromIndex(int, SAMFileHeader) - Static method in class htsjdk.samtools.SAMRecord

Static method that resolves and returns the reference name corresponding to a given reference index.

resourceAvailable(URL) - Static method in class htsjdk.samtools.util.ftp.FTPUtils
 
resourceAvailable(URL) - Static method in class htsjdk.samtools.util.HttpUtils
 
resourceExists(String) - Static method in class htsjdk.tribble.util.ParsingUtils
 
ResourceLimitedMap<Key,Value> - Class in htsjdk.samtools.util

LRU collection class for managing objects that place some resource burden such that not too many of them
 can existing in the VM at one time, but they can be reconstructed ias necessary.

ResourceLimitedMap(int, ResourceLimitedMapFunctor<Key, Value>) - Constructor for class htsjdk.samtools.util.ResourceLimitedMap

Create LRU cache

ResourceLimitedMapFunctor<Key,Value> - Interface in htsjdk.samtools.util

c.f.

restoreQualityScores(byte, List<CramCompressionRecord>) - Static method in class htsjdk.samtools.cram.build.CramNormalizer
 
retainAll(Collection<?>) - Method in class htsjdk.samtools.util.DiskBackedQueue

Not supported.

retainAll(Collection<?>) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
retr(String) - Method in class htsjdk.samtools.util.ftp.FTPClient
 
reverse(byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
 
reverse(List<T>) - Static method in class htsjdk.variant.utils.GeneralUtils
 
reverseComplement() - Method in class htsjdk.samtools.SAMRecord

Reverse-complement bases and reverse quality scores along with known optional attributes that
 need the same treatment.

reverseComplement(boolean) - Method in class htsjdk.samtools.SAMRecord

Reverse-complement bases and reverse quality scores along with known optional attributes that
 need the same treatment.

reverseComplement(Collection<String>, Collection<String>, boolean) - Method in class htsjdk.samtools.SAMRecord

Reverse complement bases and reverse quality scores.

reverseComplement(SAMRecord) - Static method in class htsjdk.samtools.SAMRecordUtil

Deprecated.
Reverse-complement bases and reverse quality scores along with known optional attributes that
 need the same treatment.

reverseComplement(SAMRecord, boolean) - Static method in class htsjdk.samtools.SAMRecordUtil

Deprecated.
Reverse-complement bases and reverse quality scores along with known optional attributes that
 need the same treatment.

reverseComplement(SAMRecord, Collection<String>, Collection<String>, boolean) - Static method in class htsjdk.samtools.SAMRecordUtil

Deprecated.
Reverse complement bases and reverse quality scores.

reverseComplement(String) - Static method in class htsjdk.samtools.util.SequenceUtil

Calculate the reverse complement of the specified sequence
 (Stolen from Reseq)

reverseComplement(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil

Reverses and complements the bases in place.

reverseComplement(byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
 
reverseComplementSqArray(byte[]) - Static method in class htsjdk.samtools.SQTagUtil

Reverses and complements the sqValues in place.

reverseIterator() - Method in class htsjdk.samtools.util.IntervalTree

Return an iterator over the entire tree that returns intervals in reverse order.

reverseIterator(int, int) - Method in class htsjdk.samtools.util.IntervalTree

Return an iterator over all intervals less than or equal to the specified interval, in reverse order.

reverseQualities(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil

Reverses the quals in place.

reverseString(String) - Static method in class htsjdk.samtools.util.StringUtil

Reverse the given string.

RevIterator(IntervalTree.Node<V>) - Constructor for class htsjdk.samtools.util.IntervalTree.RevIterator
 
RG - Variable in class htsjdk.samtools.SAMTagUtil
 
rmAttribute(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Removes key if present in the attributes

rmAttributes(List<String>) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Removes list of keys if present in the attributes

RMS_BASE_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
RMS_MAPPING_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
RunningStat() - Constructor for class htsjdk.tribble.util.MathUtils.RunningStat
 
RuntimeEOFException - Exception in htsjdk.samtools.util

Thrown by various codecs to indicate EOF without having to clutter the API with throws clauses

RuntimeEOFException() - Constructor for exception htsjdk.samtools.util.RuntimeEOFException
 
RuntimeEOFException(String) - Constructor for exception htsjdk.samtools.util.RuntimeEOFException
 
RuntimeEOFException(String, Throwable) - Constructor for exception htsjdk.samtools.util.RuntimeEOFException
 
RuntimeEOFException(Throwable) - Constructor for exception htsjdk.samtools.util.RuntimeEOFException
 
RuntimeIOException - Exception in htsjdk.samtools.util

Thrown by various IO classes to indicate IOException without having to clutter the API with throws clauses

RuntimeIOException() - Constructor for exception htsjdk.samtools.util.RuntimeIOException
 
RuntimeIOException(String) - Constructor for exception htsjdk.samtools.util.RuntimeIOException
 
RuntimeIOException(String, Throwable) - Constructor for exception htsjdk.samtools.util.RuntimeIOException
 
RuntimeIOException(Throwable) - Constructor for exception htsjdk.samtools.util.RuntimeIOException
 
RuntimeScriptException - Exception in htsjdk.samtools.util

Thrown by classes handling script engines like the javascript-based filters for SAM/VCF

RuntimeScriptException() - Constructor for exception htsjdk.samtools.util.RuntimeScriptException
 
RuntimeScriptException(String) - Constructor for exception htsjdk.samtools.util.RuntimeScriptException
 
RuntimeScriptException(String, Throwable) - Constructor for exception htsjdk.samtools.util.RuntimeScriptException
 
RuntimeScriptException(Throwable) - Constructor for exception htsjdk.samtools.util.RuntimeScriptException
 
runWithIndex(File, FeatureCodec, int) - Static method in class htsjdk.tribble.example.CountRecords
 




S

S2 - Variable in class htsjdk.samtools.SAMTagUtil
 
SA - Variable in class htsjdk.samtools.SAMTagUtil
 
SAM - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
 
Sam2CramRecordFactory - Class in htsjdk.samtools.cram.build
 
Sam2CramRecordFactory(byte[], SAMFileHeader, Version) - Constructor for class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
SAM_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
 
SAM_FLAG_FIELD_FORMAT - Static variable in class htsjdk.samtools.Defaults

The output format of the flag field when writing SAM text.

SAM_FLAGS - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
 
SAM_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
 
SAMBinaryTagAndUnsignedArrayValue - Class in htsjdk.samtools

Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because
 signedness cannot be determined by introspection of value.

SAMBinaryTagAndUnsignedArrayValue(short, Object) - Constructor for class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue
 
SAMBinaryTagAndValue - Class in htsjdk.samtools

Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.

SAMBinaryTagAndValue(short, Object) - Constructor for class htsjdk.samtools.SAMBinaryTagAndValue
 
sameGenotype(Genotype) - Method in class htsjdk.variant.variantcontext.Genotype
 
sameGenotype(Genotype, boolean) - Method in class htsjdk.variant.variantcontext.Genotype
 
sameLineTypeAndName(VCFCompoundHeaderLine) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
SAMException - Exception in htsjdk.samtools
 
SAMException() - Constructor for exception htsjdk.samtools.SAMException
 
SAMException(String) - Constructor for exception htsjdk.samtools.SAMException
 
SAMException(String, Throwable) - Constructor for exception htsjdk.samtools.SAMException
 
SAMException(Throwable) - Constructor for exception htsjdk.samtools.SAMException
 
SAMFileHeader - Class in htsjdk.samtools

Header information from a SAM or BAM file.

SAMFileHeader() - Constructor for class htsjdk.samtools.SAMFileHeader
 
SAMFileHeader(SAMSequenceDictionary) - Constructor for class htsjdk.samtools.SAMFileHeader

Constructor that initializes the sequence dictionary with the provided one.

SAMFileHeader.GroupOrder - Enum in htsjdk.samtools
 
SAMFileHeader.PgIdGenerator - Class in htsjdk.samtools

Little class to generate program group IDs

SAMFileHeader.SortOrder - Enum in htsjdk.samtools

Ways in which a SAM or BAM may be sorted.

SamFileHeaderMerger - Class in htsjdk.samtools

Merges SAMFileHeaders that have the same sequences into a single merged header
 object while providing read group translation for cases where read groups
 clash across input headers.

SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder) - Constructor for class htsjdk.samtools.SamFileHeaderMerger

Deprecated.
replaced by SamFileHeaderMerger.SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)


SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean) - Constructor for class htsjdk.samtools.SamFileHeaderMerger

Deprecated.
replaced by SamFileHeaderMerger.SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)


SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection<SAMFileHeader>, boolean) - Constructor for class htsjdk.samtools.SamFileHeaderMerger

Create SAMFileHeader with additional information..

SamFiles - Class in htsjdk.samtools
 
SamFiles() - Constructor for class htsjdk.samtools.SamFiles
 
SAMFileSource - Class in htsjdk.samtools

Represents the origin of a SAM record.

SAMFileSource(SamReader, SAMFileSpan) - Constructor for class htsjdk.samtools.SAMFileSource

Create a new SAMFileSource with the given reader and file pointer.

SAMFileSpan - Interface in htsjdk.samtools

A interface representing a collection of (possibly) discontinuous segments in the
 BAM file, possibly representing the results of an index query.

SamFileValidator - Class in htsjdk.samtools

Validates SAM files as follows:
 
 checks sam file header for sequence dictionary
 checks sam file header for read groups
 for each sam record
 
 reports error detected by SAMRecord.isValid()
 validates NM (nucleotide differences) exists and matches reality
 validates mate fields agree with data in the mate record
 
 
 

SamFileValidator(PrintWriter, int) - Constructor for class htsjdk.samtools.SamFileValidator
 
SamFileValidator.ValidationMetrics - Class in htsjdk.samtools
 
SAMFileWriter - Interface in htsjdk.samtools

Interface for SAMText and BAM file writers.

SAMFileWriterFactory - Class in htsjdk.samtools

Create a writer for writing SAM, BAM, or CRAM files.

SAMFileWriterFactory() - Constructor for class htsjdk.samtools.SAMFileWriterFactory

simple constructor

SAMFileWriterFactory(SAMFileWriterFactory) - Constructor for class htsjdk.samtools.SAMFileWriterFactory

copy constructor

SAMFileWriterImpl - Class in htsjdk.samtools

Base class for implementing SAM writer with any underlying format.

SAMFileWriterImpl() - Constructor for class htsjdk.samtools.SAMFileWriterImpl
 
SAMFlag - Enum in htsjdk.samtools

SAM flags as enum, to be used in GUI, menu, etc...

SamFlagField - Enum in htsjdk.samtools

This determines how flag fields are represented in the SAM file.

SAMFormatException - Exception in htsjdk.samtools

Thrown when a SAM file being read or decoded (text or binary) looks bad.

SAMFormatException() - Constructor for exception htsjdk.samtools.SAMFormatException
 
SAMFormatException(String) - Constructor for exception htsjdk.samtools.SAMFormatException
 
SAMFormatException(String, Throwable) - Constructor for exception htsjdk.samtools.SAMFormatException
 
SAMFormatException(Throwable) - Constructor for exception htsjdk.samtools.SAMFormatException
 
SAMHeaderRecordComparator<T extends AbstractSAMHeaderRecord> - Class in htsjdk.samtools

Provides ordering based on SAM header records' attribute values.

SAMHeaderRecordComparator(String...) - Constructor for class htsjdk.samtools.SAMHeaderRecordComparator
 
SamIndexes - Enum in htsjdk.samtools

A helper class to read BAI and CRAI indexes.

SamInputResource - Class in htsjdk.samtools

Describes a SAM-like resource, including its data (where the records are), and optionally an index.

SAMLineParser - Class in htsjdk.samtools

This class enables creation of a SAMRecord object from a String in SAM text format.

SAMLineParser(SAMFileHeader) - Constructor for class htsjdk.samtools.SAMLineParser

Public constructor.

SAMLineParser(SAMFileHeader, SamReader, File) - Constructor for class htsjdk.samtools.SAMLineParser

Public constructor.

SAMLineParser(SAMRecordFactory, ValidationStringency, SAMFileHeader, SamReader, File) - Constructor for class htsjdk.samtools.SAMLineParser

Public constructor.

SamLocusIterator - Class in htsjdk.samtools.util

Iterator that traverses a SAM File, accumulating information on a per-locus basis.

SamLocusIterator(SamReader) - Constructor for class htsjdk.samtools.util.SamLocusIterator

Prepare to iterate through the given SAM records, skipping non-primary alignments.

SamLocusIterator(SamReader, IntervalList) - Constructor for class htsjdk.samtools.util.SamLocusIterator

Prepare to iterate through the given SAM records, skipping non-primary alignments.

SamLocusIterator(SamReader, IntervalList, boolean) - Constructor for class htsjdk.samtools.util.SamLocusIterator

Prepare to iterate through the given SAM records, skipping non-primary alignments

SamLocusIterator.LocusInfo - Class in htsjdk.samtools.util

The unit of iteration.

SamLocusIterator.RecordAndOffset - Class in htsjdk.samtools.util

Implementation of AbstractRecordAndOffset class for SamLocusIterator.

SamPairUtil - Class in htsjdk.samtools

Utility methods for pairs of SAMRecords

SamPairUtil() - Constructor for class htsjdk.samtools.SamPairUtil
 
SamPairUtil.PairOrientation - Enum in htsjdk.samtools

The possible orientations of paired reads.

SamPairUtil.SetMateInfoIterator - Class in htsjdk.samtools

A class to iterate through SAMRecords and set mate information on the given records, and optionally
 set the mate cigar tag (true by default).

SAMPLE_NUMBER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
sampleNamesInOrder - Variable in class htsjdk.variant.variantcontext.GenotypesContext

sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical order

sampleNameToOffset - Variable in class htsjdk.variant.variantcontext.GenotypesContext

a map optimized for efficient lookup.

samplesWereAlreadySorted() - Method in class htsjdk.variant.vcf.VCFHeader

were the input samples sorted originally?

SAMProgramRecord - Class in htsjdk.samtools

In-memory representation of @PG SAM header record.

SAMProgramRecord(String) - Constructor for class htsjdk.samtools.SAMProgramRecord
 
SAMProgramRecord(String, SAMProgramRecord) - Constructor for class htsjdk.samtools.SAMProgramRecord
 
SamReader - Interface in htsjdk.samtools

Describes functionality for objects that produce SAMRecords and associated information.

SamReader.AssertingIterator - Class in htsjdk.samtools
 
SamReader.Indexing - Interface in htsjdk.samtools

Facet for index-related operations.

SamReader.PrimitiveSamReader - Interface in htsjdk.samtools

The minimal subset of functionality needed for a SAMRecord data source.

SamReader.PrimitiveSamReaderToSamReaderAdapter - Class in htsjdk.samtools

Decorator for a SamReader.PrimitiveSamReader that expands its functionality into a SamReader,
 given the backing SamInputResource.

SamReader.ReaderImplementation - Class in htsjdk.samtools

Internal interface for SAM/BAM/CRAM file reader implementations,
 as distinct from non-file-based readers.

SamReader.Type - Class in htsjdk.samtools

Describes a type of SAM file.

SamReaderFactory - Class in htsjdk.samtools

Describes the functionality for producing SamReader, and offers a
 handful of static generators.

SamReaderFactory() - Constructor for class htsjdk.samtools.SamReaderFactory
 
SamReaderFactory.Option - Enum in htsjdk.samtools

A collection of binary SamReaderFactory options.

SAMReadGroupRecord - Class in htsjdk.samtools

Header information about a read group.

SAMReadGroupRecord(String) - Constructor for class htsjdk.samtools.SAMReadGroupRecord
 
SAMReadGroupRecord(String, SAMReadGroupRecord) - Constructor for class htsjdk.samtools.SAMReadGroupRecord
 
SAMReadGroupRecord.PlatformValue - Enum in htsjdk.samtools
 
SAMRecord - Class in htsjdk.samtools

Java binding for a SAM file record.

SAMRecord(SAMFileHeader) - Constructor for class htsjdk.samtools.SAMRecord
 
SAMRecord.SAMTagAndValue - Class in htsjdk.samtools

Tag name and value of an attribute, for getAttributes() method.

SAMRecordComparator - Interface in htsjdk.samtools

Interface for comparators that define the various SAM sort orders.

SAMRecordCoordinateComparator - Class in htsjdk.samtools

Comparator for sorting SAMRecords by coordinate.

SAMRecordCoordinateComparator() - Constructor for class htsjdk.samtools.SAMRecordCoordinateComparator
 
SAMRecordDuplicateComparator - Class in htsjdk.samtools

Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates).

SAMRecordDuplicateComparator() - Constructor for class htsjdk.samtools.SAMRecordDuplicateComparator
 
SAMRecordDuplicateComparator(List<SAMFileHeader>) - Constructor for class htsjdk.samtools.SAMRecordDuplicateComparator
 
samRecordFactory(SAMRecordFactory) - Method in class htsjdk.samtools.SamReaderFactory

Set this factory's SAMRecordFactory to the provided one, then returns itself.

SAMRecordFactory - Interface in htsjdk.samtools

Factory interface which allows plugging in of different classes for generating instances of
 SAMRecord and BAMRecord when reading from SAM/BAM files.

SamRecordFilter - Interface in htsjdk.samtools.filter

API for filtering SAMRecords

 $Id$

SamRecordIntervalIteratorFactory - Class in htsjdk.samtools.util

Create an iterator over a SamReader that only returns reads that overlap one of the intervals
 in an interval list.

SamRecordIntervalIteratorFactory() - Constructor for class htsjdk.samtools.util.SamRecordIntervalIteratorFactory
 
SAMRecordIterator - Interface in htsjdk.samtools

A general interface that adds functionality to a CloseableIterator of
 SAMRecords.

SAMRecordQueryHashComparator - Class in htsjdk.samtools

SAMRecord comparator that provides an ordering based on a hash of the queryname.

SAMRecordQueryHashComparator() - Constructor for class htsjdk.samtools.SAMRecordQueryHashComparator
 
SAMRecordQueryNameComparator - Class in htsjdk.samtools

Comparator for "queryname" ordering of SAMRecords.

SAMRecordQueryNameComparator() - Constructor for class htsjdk.samtools.SAMRecordQueryNameComparator
 
SAMRecordSetBuilder - Class in htsjdk.samtools

Factory class for creating SAMRecords for testing purposes.

SAMRecordSetBuilder() - Constructor for class htsjdk.samtools.SAMRecordSetBuilder

Constructs a new SAMRecordSetBuilder with all the data needed to keep the records
 sorted in coordinate order.

SAMRecordSetBuilder(boolean, SAMFileHeader.SortOrder) - Constructor for class htsjdk.samtools.SAMRecordSetBuilder

Construct a new SAMRecordSetBuilder.

SAMRecordSetBuilder(boolean, SAMFileHeader.SortOrder, boolean) - Constructor for class htsjdk.samtools.SAMRecordSetBuilder
 
SAMRecordSetBuilder(boolean, SAMFileHeader.SortOrder, boolean, int) - Constructor for class htsjdk.samtools.SAMRecordSetBuilder
 
SAMRecordSetBuilder(boolean, SAMFileHeader.SortOrder, boolean, int, DuplicateScoringStrategy.ScoringStrategy) - Constructor for class htsjdk.samtools.SAMRecordSetBuilder
 
SamRecordTrackingBuffer<T extends SamRecordWithOrdinal> - Class in htsjdk.samtools.util

This class stores SAMRecords for return.

SamRecordTrackingBuffer(int, int, List<File>, SAMFileHeader, Class<T>) - Constructor for class htsjdk.samtools.util.SamRecordTrackingBuffer
 
SAMRecordUtil - Class in htsjdk.samtools

Deprecated.

SAMRecordUtil() - Constructor for class htsjdk.samtools.SAMRecordUtil

Deprecated.
 
SamRecordWithOrdinal - Class in htsjdk.samtools.util

A little class to store the unique index associated with this record.

SamRecordWithOrdinal() - Constructor for class htsjdk.samtools.util.SamRecordWithOrdinal
 
SamRecordWithOrdinal(SAMRecord, long) - Constructor for class htsjdk.samtools.util.SamRecordWithOrdinal
 
SAMSequenceDictionary - Class in htsjdk.samtools

Collection of SAMSequenceRecords.

SAMSequenceDictionary() - Constructor for class htsjdk.samtools.SAMSequenceDictionary
 
SAMSequenceDictionary(List<SAMSequenceRecord>) - Constructor for class htsjdk.samtools.SAMSequenceDictionary
 
SAMSequenceDictionaryCodec - Class in htsjdk.samtools

"On the fly" codec SAMSequenceDictionaryCodec.

SAMSequenceDictionaryCodec(BufferedWriter) - Constructor for class htsjdk.samtools.SAMSequenceDictionaryCodec
 
SAMSequenceDictionaryExtractor - Class in htsjdk.variant.utils

Tiny class for automatically loading a SAMSequenceDictionary given a file

SAMSequenceDictionaryExtractor() - Constructor for class htsjdk.variant.utils.SAMSequenceDictionaryExtractor
 
SAMSequenceRecord - Class in htsjdk.samtools

Header information about a reference sequence.

SAMSequenceRecord(String) - Constructor for class htsjdk.samtools.SAMSequenceRecord

Deprecated.
Use SAMSequenceRecord.SAMSequenceRecord(String, int) instead.
 sequenceLength is required for the object to be considered valid.


SAMSequenceRecord(String, int) - Constructor for class htsjdk.samtools.SAMSequenceRecord
 
SAMSortOrderChecker - Class in htsjdk.samtools

Encapsulates simple check for SAMRecord order.

SAMSortOrderChecker(SAMFileHeader.SortOrder) - Constructor for class htsjdk.samtools.SAMSortOrderChecker
 
SamStreams - Class in htsjdk.samtools

Utilities related to processing of InputStreams encoding SAM data

SamStreams() - Constructor for class htsjdk.samtools.SamStreams
 
SAMTag - Enum in htsjdk.samtools

The standard tags for a SAM record that are defined in the SAM spec.

SAMTagAndValue(String, Object) - Constructor for class htsjdk.samtools.SAMRecord.SAMTagAndValue
 
SAMTagUtil - Class in htsjdk.samtools

Facility for converting between String and short representation of a SAM tag.

SAMTagUtil() - Constructor for class htsjdk.samtools.SAMTagUtil
 
SAMTestUtil - Class in htsjdk.samtools

Misc methods for SAM-related unit tests.

SAMTestUtil() - Constructor for class htsjdk.samtools.SAMTestUtil
 
SAMTestUtil.SanityCheckFailedException - Exception in htsjdk.samtools

Indicates that a required sanity-check condition was not met.

SAMTextHeaderCodec - Class in htsjdk.samtools

Parser for a SAM text header, and a generator of SAM text header.

SAMTextHeaderCodec() - Constructor for class htsjdk.samtools.SAMTextHeaderCodec
 
SAMTextWriter - Class in htsjdk.samtools

Writer for text-format SAM files.

SAMTextWriter(Writer) - Constructor for class htsjdk.samtools.SAMTextWriter

Constructs a SAMTextWriter that outputs to a Writer.

SAMTextWriter(File) - Constructor for class htsjdk.samtools.SAMTextWriter

Constructs a SAMTextWriter that writes to a File.

SAMTextWriter(OutputStream) - Constructor for class htsjdk.samtools.SAMTextWriter

Constructs a SAMTextWriter that writes to an OutputStream.

SAMTextWriter(Writer, SamFlagField) - Constructor for class htsjdk.samtools.SAMTextWriter

Constructs a SAMTextWriter that outputs to a Writer.

SAMTextWriter(File, SamFlagField) - Constructor for class htsjdk.samtools.SAMTextWriter

Constructs a SAMTextWriter that writes to a File.

SAMTextWriter(OutputStream, SamFlagField) - Constructor for class htsjdk.samtools.SAMTextWriter

Constructs a SAMTextWriter that writes to an OutputStream.

SAMTools - Class in htsjdk.samtools

Command line utility for manipulating SAM/BAM files.

SAMUtils - Class in htsjdk.samtools

Utilty methods.

SAMUtils() - Constructor for class htsjdk.samtools.SAMUtils
 
SAMValidationError - Class in htsjdk.samtools

Class that encapsulates a validation error message as well as a type code so that
 errors can be aggregated by type.

SAMValidationError(SAMValidationError.Type, String, String) - Constructor for class htsjdk.samtools.SAMValidationError

Construct a SAMValidationError with unknown record number.

SAMValidationError(SAMValidationError.Type, String, String, long) - Constructor for class htsjdk.samtools.SAMValidationError

Construct a SAMValidationError with possibly-known record number.

SAMValidationError.Severity - Enum in htsjdk.samtools
 
SAMValidationError.Type - Enum in htsjdk.samtools
 
sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile

Do some basic checking to make sure the dictionary and the index match.

SanityCheckFailedException(String) - Constructor for exception htsjdk.samtools.SAMTestUtil.SanityCheckFailedException
 
scoreIndexes(double, Map<IndexFactory.IndexType, TribbleIndexCreator>, int, IndexFactory.IndexBalanceApproach) - Static method in class htsjdk.tribble.index.DynamicIndexCreator

score the available indexes for the specified density and feature lengths

 The scoring method is trying to determine how many features would be returned for a sample one base query; or:
 (features/seek).

Scores - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing a contiguous stretch of quality scores in a read.

Scores() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
Scores(int, byte[]) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
scoresCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
SECOND_OF_PAIR_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
SecondaryAlignmentFilter - Class in htsjdk.samtools.filter

SamRecordFilter that filters out secondary alignments, but not supplemental alignments.

SecondaryAlignmentFilter() - Constructor for class htsjdk.samtools.filter.SecondaryAlignmentFilter
 
SecondaryOrSupplementaryFilter - Class in htsjdk.samtools.filter

Filter out SAMRecords with NotPrimaryAlignment or Supplementary flag set
 This class should be viewed as a replacement for NotPrimarySkippingIterator,
 in that we did not want to change the functionality of NPSI to no longer match its name
 $Id$

SecondaryOrSupplementaryFilter() - Constructor for class htsjdk.samtools.filter.SecondaryOrSupplementaryFilter
 
SecondaryOrSupplementarySkippingIterator - Class in htsjdk.samtools

Wrapper around SAMRecord iterator that skips over secondary and supplementary elements.

SecondaryOrSupplementarySkippingIterator(CloseableIterator<SAMRecord>) - Constructor for class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
 
seek(long) - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
 
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
 
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
 
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
 
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableStream
 
seek(long) - Method in class htsjdk.samtools.util.BlockCompressedInputStream

Seek to the given position in the file.

SeekableBufferedStream - Class in htsjdk.samtools.seekablestream

A wrapper class to provide buffered read access to a SeekableStream.

SeekableBufferedStream(SeekableStream, int) - Constructor for class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
SeekableBufferedStream(SeekableStream) - Constructor for class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
SeekableFileStream - Class in htsjdk.samtools.seekablestream
 
SeekableFileStream(File) - Constructor for class htsjdk.samtools.seekablestream.SeekableFileStream
 
SeekableFTPStream - Class in htsjdk.samtools.seekablestream

Unfortunately the seekable stream classes exist for both Tribble and Picard, and we need both.

SeekableFTPStream(URL) - Constructor for class htsjdk.samtools.seekablestream.SeekableFTPStream
 
SeekableFTPStream(URL, UserPasswordInput) - Constructor for class htsjdk.samtools.seekablestream.SeekableFTPStream
 
SeekableFTPStreamHelper - Class in htsjdk.samtools.seekablestream
 
SeekableHTTPStream - Class in htsjdk.samtools.seekablestream
 
SeekableHTTPStream(URL) - Constructor for class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
SeekableHTTPStream(URL, Proxy) - Constructor for class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
SeekableMemoryStream - Class in htsjdk.samtools.seekablestream
 
SeekableMemoryStream(byte[], String) - Constructor for class htsjdk.samtools.seekablestream.SeekableMemoryStream
 
SeekablePathStream - Class in htsjdk.samtools.seekablestream

An implementation of SeekableStream for Path.

SeekablePathStream(Path) - Constructor for class htsjdk.samtools.seekablestream.SeekablePathStream
 
SeekableStream - Class in htsjdk.samtools.seekablestream
 
SeekableStream() - Constructor for class htsjdk.samtools.seekablestream.SeekableStream
 
SeekableStreamFactory - Class in htsjdk.samtools.seekablestream

Singleton class for getting SeekableStreams from URL/paths
 Applications using this library can set their own factory

SEPARATOR - Static variable in class htsjdk.samtools.metrics.MetricsFile
 
SEQUENCE_HEADER - Static variable in class htsjdk.samtools.fastq.FastqConstants
 
SEQUENCE_LENGTH_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
 
SEQUENCE_NAME_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
 
sequenceColumn - Variable in class htsjdk.tribble.index.tabix.TabixFormat

One-based index of the column in the file being indexed containing the sequence name

sequenceDictionary - Variable in class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
sequenceId - Variable in class htsjdk.samtools.cram.CRAIEntry
 
sequenceId - Variable in class htsjdk.samtools.cram.structure.Container
 
sequenceId - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
sequenceId - Variable in class htsjdk.samtools.cram.structure.Slice
 
SequenceListsDifferException() - Constructor for exception htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
 
SequenceListsDifferException(String) - Constructor for exception htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
 
SequenceListsDifferException(String, Throwable) - Constructor for exception htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
 
SequenceListsDifferException(Throwable) - Constructor for exception htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
 
sequenceName - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
SequenceUtil - Class in htsjdk.samtools.util
 
SequenceUtil() - Constructor for class htsjdk.samtools.util.SequenceUtil
 
SequenceUtil.SequenceListsDifferException - Exception in htsjdk.samtools.util
 
SEQUENCING_CENTER_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
serializeAndDeserialize(T) - Static method in class htsjdk.samtools.util.TestUtil

Serialize and Deserialize an object
 Useful for testing if serialization is correctly handled for a class.

serialVersionUID - Static variable in class htsjdk.samtools.AbstractSAMHeaderRecord
 
serialVersionUID - Static variable in class htsjdk.samtools.AlignmentBlock
 
serialVersionUID - Static variable in class htsjdk.samtools.Cigar
 
serialVersionUID - Static variable in class htsjdk.samtools.CigarElement
 
serialVersionUID - Static variable in class htsjdk.samtools.SAMBinaryTagAndValue
 
serialVersionUID - Static variable in class htsjdk.samtools.SAMRecord
 
serialVersionUID - Static variable in class htsjdk.samtools.SAMSequenceDictionary
 
serialVersionUID - Static variable in class htsjdk.samtools.SAMSequenceRecord
 
serialVersionUID - Static variable in class htsjdk.samtools.SAMValidationError
 
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.Allele
 
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.CommonInfo
 
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.Genotype
 
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.GenotypesContext
 
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.VariantContext
 
serialVersionUID - Static variable in class htsjdk.variant.vcf.VCFHeader
 
serialVersionUID - Static variable in class htsjdk.variant.vcf.VCFHeaderLine
 
set(int, Genotype) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
setAlignmentStart(int) - Method in class htsjdk.samtools.SAMRecord
 
setAlignmentStart(int) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setAllowMissingFieldsInHeader(boolean) - Method in class htsjdk.variant.vcf.VCFEncoder

Deprecated.

setAppVersionString(String) - Static method in class htsjdk.samtools.sra.SRAAccession

Sets an app version string which will let SRA know which software uses it.

setAssembly(String) - Method in class htsjdk.samtools.SAMSequenceRecord
 
setAsyncOutputBufferSize(int) - Method in class htsjdk.samtools.SAMFileWriterFactory

If and only if using asynchronous IO then sets the maximum number of records that can be buffered per
 SAMFileWriter before producers will block when trying to write another SAMRecord.

setAttribute(String, Object) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord

Deprecated.
Use {@link #setAttribute(String, String) instead


setAttribute(String, String) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord

Set the given value for the attribute named 'key'.

setAttribute(short, Object, boolean) - Method in class htsjdk.samtools.BAMRecord
 
setAttribute(String, Object) - Method in class htsjdk.samtools.cram.structure.Slice

Set a value for the tag.

setAttribute(String, Object) - Method in class htsjdk.samtools.SAMRecord

Set a named attribute onto the SAMRecord.

setAttribute(short, Object) - Method in class htsjdk.samtools.SAMRecord
 
setAttribute(short, Object, boolean) - Method in class htsjdk.samtools.SAMRecord
 
setAttribute(short, Object) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setAttribute(short, Object, boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setAttributes(SAMBinaryTagAndValue) - Method in class htsjdk.samtools.SAMRecord

Replace any existing attributes with the given linked item.

setAttributes(SAMBinaryTagAndValue) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setAttributes(Map<String, ?>) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
setBase(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
setBase(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
setBase(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
setBaseQualities(byte[]) - Method in class htsjdk.samtools.BAMRecord
 
setBaseQualities(byte[]) - Method in class htsjdk.samtools.SAMRecord
 
setBaseQualities(byte[]) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setBaseQualityString(String) - Method in class htsjdk.samtools.SAMRecord
 
setBases(byte[]) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
 
setBinLabel(String) - Method in class htsjdk.samtools.util.Histogram
 
setBisulfiteSequenced(boolean) - Method in class htsjdk.samtools.SamFileValidator
 
setBuffer(int) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set a buffer size for the file output stream passed to the next VariantContextWriter created by this builder.

setBufferSize(int) - Method in class htsjdk.samtools.SAMFileWriterFactory

Controls size of write buffer.

setCaptureAllTags(boolean) - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
setCaptureAllTags(boolean) - Method in class htsjdk.samtools.CRAMFileWriter
 
setCaptureReadNames(boolean) - Method in class htsjdk.samtools.cram.encoding.writer.Writer
 
setCaptureTags(Set<String>) - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
setCaptureTags(Set<String>) - Method in class htsjdk.samtools.CRAMFileWriter
 
setCheckCrcs(boolean) - Method in class htsjdk.samtools.util.BlockCompressedInputStream

Determines whether or not the inflater will re-calculated the CRC on the decompressed data
 and check it against the value stored in the GZIP header.

setCheckCrcs(boolean) - Method in class htsjdk.samtools.util.BlockGunzipper

Allows the caller to decide whether or not to check CRCs on when uncompressing blocks.

setChr(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setChrIndex(List<IntervalTreeIndex.ChrIndex>) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
 
setChunkEnd(long) - Method in class htsjdk.samtools.Chunk
 
setChunkList(List<Chunk>) - Method in class htsjdk.samtools.Bin

Sets the chunks associated with this bin

setChunkStart(long) - Method in class htsjdk.samtools.Chunk
 
setCigar(Cigar) - Method in class htsjdk.samtools.BAMRecord
 
setCigar(Cigar) - Method in class htsjdk.samtools.SAMRecord
 
setCigar(Cigar) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setCigarString(String) - Method in class htsjdk.samtools.BAMRecord
 
setCigarString(String) - Method in class htsjdk.samtools.SAMRecord
 
setCigarString(String) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setCode(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
setCodingEnd(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon

Method description

setCodingEnd(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Method description

setCodingStart(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon

Method description

setCodingStart(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Method description

setColor(Color) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setCommandLine(String) - Method in class htsjdk.samtools.SAMProgramRecord
 
setComments(Collection<String>) - Method in class htsjdk.samtools.SAMFileHeader

Replace existing comments with the contents of the given collection.

setComponentMethods(AbstractFeatureReader.ComponentMethods) - Static method in class htsjdk.tribble.AbstractFeatureReader
 
setCompressionLevel(int) - Method in class htsjdk.samtools.SAMFileWriterFactory

set compression level 0!none 9: max

setCompressionLevel(int) - Static method in class htsjdk.samtools.util.IOUtil

Sets the GZip compression level for subsequent GZIPOutputStream object creation.

setContent(byte[], byte[]) - Method in class htsjdk.samtools.cram.structure.Block
 
setContentId(int) - Method in class htsjdk.samtools.cram.structure.Block
 
setContentType(BlockContentType) - Method in class htsjdk.samtools.cram.structure.Block
 
setCreateIndex(boolean) - Method in class htsjdk.samtools.SAMFileWriterFactory

Convenience method allowing newSAMFileWriterFactory().setCreateIndex(true);
 Equivalent to SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true); newSAMFileWriterFactory();
 If a BAM or CRAM (not SAM) file is created, the setting is true, and the file header specifies coordinate order,
 then a BAM index file will be written along with the BAM file.

setCreateMd5(boolean) - Method in class htsjdk.samtools.fastq.FastqWriterFactory

If true, compute MD5 and write appropriately-named file when file is closed.

setCreateMD5(boolean) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Choose whether to also create an MD5 digest file for the next VariantContextWriter created by this builder.

setCreateMD5() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Create an MD5 digest file for the next VariantContextWriter created by this builder.

setCreateMd5File(boolean) - Method in class htsjdk.samtools.SAMFileWriterFactory

Sets whether to create md5Files for BAMs from this factory.

setDate(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

setDefaultCompressionLevel(int) - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream

Sets the GZip compression level for subsequent BlockCompressedOutputStream object creation
 that do not specify the compression level.

setDefaultCreateIndexWhileWriting(boolean) - Static method in class htsjdk.samtools.SAMFileWriterFactory

Sets the default for subsequent SAMFileWriterFactories
 that do not specify whether to create an index.

setDefaultCreateMd5File(boolean) - Static method in class htsjdk.samtools.SAMFileWriterFactory

Sets the default for whether to create md5Files for BAM files this factory.

setDefaultDeflaterFactory(DeflaterFactory) - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream

Sets the default DeflaterFactory that will be used for all instances unless specified otherwise in the constructor.

setDefaultMaxRecordsInRam(int) - Static method in class htsjdk.samtools.SAMFileWriterImpl

When writing records that are not presorted, specify the number of records stored in RAM
 before spilling to disk.

setDefaultOption(Options) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Add one option to the set of default Options that will be used as the initial set of options
 for all VariantContextWriterBuilders created after this call.

setDefaultValidationStringency(ValidationStringency) - Static method in class htsjdk.samtools.SamReaderFactory
 
setDeflaterFactory(DeflaterFactory) - Method in class htsjdk.samtools.SAMFileWriterFactory

Set the deflater factory used by BAM writers created by this writer factory.

setDescription(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setDescription(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setDestructiveIteration(boolean) - Method in class htsjdk.samtools.util.SortingCollection

Tell this collection that it is allowed to discard data during iteration in order to reduce memory footprint,
 precluding a second iteration.

setDetached(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setDownloadTriesBeforeFailing(int) - Method in class htsjdk.samtools.cram.ref.ReferenceSource
 
setDuplicate(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setDuplicateFlag(boolean) - Method in class htsjdk.samtools.DuplicateSet

Controls if we should update the duplicate flag of the records in this set.

setDuplicateReadFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the read is either a PCR duplicate or an optical duplicate.

setEmitUncoveredLoci(boolean) - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
setEmitUncoveredLoci(boolean) - Method in class htsjdk.samtools.util.EdgeReadIterator

For correct work of EdgeReadIterator value emitUncoveredLoci must be true.

setEnd(int) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setEndPosition(long) - Method in class htsjdk.tribble.index.Block

This method is used to aid in consolidating blocks.

setErrorsToIgnore(Collection<SAMValidationError.Type>) - Method in class htsjdk.samtools.SamFileValidator

Sets one or more error types that should not be reported on.

setExons(List<FullBEDFeature.Exon>) - Method in class htsjdk.tribble.bed.FullBEDFeature
 
setFileSource(SamReader) - Method in class htsjdk.samtools.CRAMIterator
 
setFileSource(SAMFileSource) - Method in class htsjdk.samtools.SAMRecord

Sets a marker providing the source reader for this file and the position in the file from which the read originated.

setFirstOfPairFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the read is the first read in a pair.

setFirstOfPairFlag(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setFirstSegment(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setFlags(int) - Method in class htsjdk.samtools.SAMRecord
 
setFlags(int) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setFlowOrder(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setForcePreserveQualityScores(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setGlobalLogLevel(Log.LogLevel) - Static method in class htsjdk.samtools.util.Log
 
setGroupOrder(SAMFileHeader.GroupOrder) - Method in class htsjdk.samtools.SAMFileHeader
 
setHasMateDownStream(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setHeader(SAMFileHeader) - Method in class htsjdk.samtools.SAMFileWriterImpl

Must be called before addAlignment.

setHeader(SAMFileHeader) - Method in class htsjdk.samtools.SAMRecord

Sets the SAMFileHeader for this record.

setHeader(SAMFileHeader) - Method in class htsjdk.samtools.SAMRecordSetBuilder
 
setHeaderStrict(SAMFileHeader) - Method in class htsjdk.samtools.SAMRecord

Establishes the SAMFileHeader for this record and forces resolution of the record's reference and mate reference
 names against the header using the sequence dictionary in the new header.

setHistogram(Histogram<HKEY>) - Method in class htsjdk.samtools.metrics.MetricsFile

Sets the histogram contained in the metrics file.

setHost(String) - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
 
setHours(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

setID(String) - Method in class htsjdk.samtools.cram.structure.CramHeader

Set the id of the header.

setIgnoreTags(Set<String>) - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
setIgnoreTags(Set<String>) - Method in class htsjdk.samtools.CRAMFileWriter
 
setIgnoreWarnings(boolean) - Method in class htsjdk.samtools.SamFileValidator
 
setIncludeIndels(boolean) - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
setIncludeIndels(boolean) - Method in class htsjdk.samtools.util.EdgeReadIterator
 
setIncludeNonPfReads(boolean) - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
setIndex(byte) - Method in class htsjdk.samtools.cram.structure.ReadTag
 
setIndexCreator(IndexCreator) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set an IndexCreator for the next VariantContextWriter created by this builder.

setIndexSequenceDictionary(SAMSequenceDictionary) - Method in interface htsjdk.tribble.index.IndexCreator

Set the sequence dictionary for the index.

setIndexSequenceDictionary(SAMSequenceDictionary) - Method in class htsjdk.tribble.index.TribbleIndexCreator

Set the sequence dictionary entries for the index property list.

setIndexValidationStringency(BamIndexValidator.IndexValidationStringency) - Method in class htsjdk.samtools.SamFileValidator
 
setInferredInsertSize(int) - Method in class htsjdk.samtools.SAMRecord
 
setInferredInsertSize(int) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setInputFileName(String) - Method in class htsjdk.samtools.util.BinaryCodec
 
setInputStream(InputStream) - Method in class htsjdk.samtools.BAMRecordCodec

Sets the input stream that records will be read from.

setInputStream(InputStream, String) - Method in class htsjdk.samtools.BAMRecordCodec

Sets the input stream that records will be read from.

setInputStream(InputStream) - Method in interface htsjdk.samtools.CoordinateSortedPairInfoMap.Codec

Where to read encoded input from

setInputStream(InputStream) - Method in class htsjdk.samtools.util.BinaryCodec
 
setInputStream(InputStream) - Method in interface htsjdk.samtools.util.SortingCollection.Codec

Where to read encoded input from

setInputStream(InputStream) - Method in class htsjdk.variant.vcf.VCFRecordCodec
 
setInstance(CustomReaderFactory) - Static method in class htsjdk.samtools.CustomReaderFactory
 
setInstance(ISeekableStreamFactory) - Static method in class htsjdk.samtools.seekablestream.SeekableStreamFactory
 
setKeySequence(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setLastChunk(Chunk) - Method in class htsjdk.samtools.Bin

Optimization to keep lastChunk instead of iterating over all chunks repeatedly

setLastSegment(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setLength(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
setLength(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
setLength(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
setLength(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
setLibrary(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setLiftOverMinMatch(double) - Method in class htsjdk.samtools.liftover.LiftOver

Set minimum fraction of bases that must remap.

setLink(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setLog10PError(double) - Method in class htsjdk.variant.variantcontext.CommonInfo
 
setMappingQuality(int) - Method in class htsjdk.samtools.SAMRecord
 
setMappingQuality(int) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setMappingQualityScoreCutoff(int) - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
setMateAlignmentStart(int) - Method in class htsjdk.samtools.SAMRecord
 
setMateAlignmentStart(int) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setMateInfo(SAMRecord, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil

Write the mate info for two SAMRecords.

setMateInfo(SAMRecord, SAMRecord, boolean) - Static method in class htsjdk.samtools.SamPairUtil

Write the mate info for two SAMRecords

setMateInfo(SAMRecord, SAMRecord, SAMFileHeader, boolean) - Static method in class htsjdk.samtools.SamPairUtil

Deprecated.
use SamPairUtil.setMateInfo(SAMRecord, SAMRecord, boolean) instead


setMateInfo(SAMRecord, SAMRecord, SAMFileHeader) - Static method in class htsjdk.samtools.SamPairUtil

Deprecated.
use SamPairUtil.setMateInfo(SAMRecord, SAMRecord) instead


SetMateInfoIterator(Iterator<SAMRecord>) - Constructor for class htsjdk.samtools.SamPairUtil.SetMateInfoIterator

By default, the mate cigar tag is set

SetMateInfoIterator(Iterator<SAMRecord>, boolean) - Constructor for class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
 
SetMateInfoIterator(Iterator<SAMRecord>, boolean, boolean) - Constructor for class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
 
setMateInformationOnSupplementalAlignment(SAMRecord, SAMRecord, boolean) - Static method in class htsjdk.samtools.SamPairUtil

Sets mate pair information appropriately on a supplemental SAMRecord (e.g.

setMateInformationOnSupplementalAlignment(SAMRecord, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil

Sets mate pair information appropriately on a supplemental SAMRecord (e.g.

setMateNegativeStrand(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setMateNegativeStrandFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

strand of the mate (false for forward; true for reverse strand).

setMateNegativeStrandFlag(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setMateReferenceIndex(int) - Method in class htsjdk.samtools.SAMRecord

Updates the mate reference index.

setMateReferenceIndex(int) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setMateReferenceName(String) - Method in class htsjdk.samtools.SAMRecord

Sets the mate reference name for this record.

setMateReferenceName(String) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setMateUnmapped(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setMateUnmappedFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the mate is unmapped.

setMateUnmappedFlag(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setMaxReadsToAccumulatePerLocus(int) - Method in class htsjdk.samtools.util.AbstractLocusIterator

If set, this will cap the number of reads we accumulate for any given position.

setMaxReadsToAccumulatePerLocus(int) - Method in class htsjdk.samtools.util.EdgeReadIterator

This method isn't supported in current implementation.

setMaxRecordsInRam(int) - Method in class htsjdk.samtools.SAMFileWriterFactory

Before creating a writer that is not presorted, this method may be called in order to override
 the default number of SAMRecords stored in RAM before spilling to disk
 (c.f.

setMd5(String) - Method in exception htsjdk.samtools.cram.ref.EnaRefService.GaveUpException
 
setMd5(String) - Method in class htsjdk.samtools.SAMSequenceRecord
 
setMD5(String) - Method in class htsjdk.tribble.index.AbstractIndex
 
setMethod(BlockCompressionMethod) - Method in class htsjdk.samtools.cram.structure.Block
 
setMinutes(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

setMonth(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

setMrnaBase(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
 
setMrnaBase(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
 
setMultiFragment(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setName(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setName(String) - Method in interface htsjdk.tribble.NameAwareCodec
 
setName(String) - Method in class htsjdk.variant.variantcontext.CommonInfo

Sets the name

setName(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec

set the name of this codec

setNegativeStrand(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setNotPrimaryAlignmentFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the alignment is not primary (a read having split hits may have multiple primary alignment records).

setNotPrimaryAlignmentFlag(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setNumber(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
 
setNumber(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
 
setNumberToUnbounded() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
 
setOption(SamReaderFactory.Option, boolean) - Method in class htsjdk.samtools.SamReaderFactory

Sets a specific Option to a boolean value.

setOption(Options) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Add one option to the set of Options for the VariantContextWriterBuilder, if it's not already present.

setOptions(EnumSet<Options>) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Replace the set of Options for the VariantContextWriterBuilder with a new set.

setOriginalBaseQualities(byte[]) - Method in class htsjdk.samtools.SAMRecord

Sets the original base quality scores into the "OQ" tag as a String.

setOutputBCFStream(OutputStream) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set the output BCF stream for the next VariantContextWriter created by this builder.

setOutputFile(File) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set the output file for the next VariantContextWriter created by this builder.

setOutputFile(String) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set the output file for the next VariantContextWriter created by this builder.

setOutputFileName(String) - Method in class htsjdk.samtools.util.BinaryCodec
 
setOutputFileType(VariantContextWriterBuilder.OutputType) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set the output file type for the next VariantContextWriter created by this builder.

setOutputStream(OutputStream) - Method in class htsjdk.samtools.BAMRecordCodec

Sets the output stream that records will be written to.

setOutputStream(OutputStream, String) - Method in class htsjdk.samtools.BAMRecordCodec

Sets the output stream that records will be written to.

setOutputStream(OutputStream) - Method in interface htsjdk.samtools.CoordinateSortedPairInfoMap.Codec

Where to write encoded output

setOutputStream(OutputStream) - Method in class htsjdk.samtools.util.BinaryCodec
 
setOutputStream(OutputStream) - Method in interface htsjdk.samtools.util.SortingCollection.Codec

Where to write encoded output

setOutputStream(OutputStream) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set the output stream (VCF, by default) for the next VariantContextWriter created by this builder.

setOutputStream(OutputStream) - Method in class htsjdk.variant.vcf.VCFRecordCodec
 
setOutputVCFStream(OutputStream) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set the output VCF stream for the next VariantContextWriter created by this builder.

setPhase(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon

Method description

setPhase(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Method description

setPlatform(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setPlatformModel(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setPlatformUnit(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
setPosition(int) - Method in interface htsjdk.samtools.cram.encoding.readfeatures.ReadFeature
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
setPosition(int) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
setPredictedMedianInsertSize(Integer) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setPreserveReadNames(boolean) - Method in class htsjdk.samtools.cram.build.ContainerFactory
 
setPreserveReadNames(boolean) - Method in class htsjdk.samtools.CRAMContainerStreamWriter
 
setPreserveReadNames(boolean) - Method in class htsjdk.samtools.CRAMFileWriter
 
setPreviousProgramGroupId(String) - Method in class htsjdk.samtools.SAMProgramRecord
 
setProgramGroup(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setProgramName(String) - Method in class htsjdk.samtools.SAMProgramRecord
 
setProgramRecord(SAMProgramRecord) - Method in class htsjdk.samtools.SAMRecordSetBuilder

Adds the given program record to the header, and assigns the PG tag to any SAMRecords
 created after it has been added.

setProgramRecords(List<SAMProgramRecord>) - Method in class htsjdk.samtools.SAMFileHeader

Replace entire list of program records

setProgramVersion(String) - Method in class htsjdk.samtools.SAMProgramRecord
 
setProgressLogger(ProgressLoggerInterface) - Method in interface htsjdk.samtools.SAMFileWriter

Sets a ProgressLogger on this writer.

setProgressLogger(ProgressLoggerInterface) - Method in class htsjdk.samtools.SAMFileWriterImpl

Sets the progress logger used by this implementation.

setProperPair(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setProperPairAndMateInfo(SAMRecord, SAMRecord, SAMFileHeader, List<SamPairUtil.PairOrientation>) - Static method in class htsjdk.samtools.SamPairUtil

Deprecated.
use SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, List) instead


setProperPairAndMateInfo(SAMRecord, SAMRecord, SAMFileHeader, List<SamPairUtil.PairOrientation>, boolean) - Static method in class htsjdk.samtools.SamPairUtil

Deprecated.
use SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean)


setProperPairAndMateInfo(SAMRecord, SAMRecord, List<SamPairUtil.PairOrientation>) - Static method in class htsjdk.samtools.SamPairUtil

This method will clear any mate cigar already present.

setProperPairAndMateInfo(SAMRecord, SAMRecord, List<SamPairUtil.PairOrientation>, boolean) - Static method in class htsjdk.samtools.SamPairUtil
 
setProperPairFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).

setProperPairFlag(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setProperPairFlags(SAMRecord, SAMRecord, List<SamPairUtil.PairOrientation>) - Static method in class htsjdk.samtools.SamPairUtil
 
setProxy(Proxy) - Static method in class htsjdk.tribble.util.HTTPHelper
 
setQualityScore(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
 
setQualityScore(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
setQualityScoreCutoff(int) - Method in class htsjdk.samtools.util.AbstractLocusIterator
 
setQualityScoreCutoff(int) - Method in class htsjdk.samtools.util.EdgeReadIterator

This method isn't supported in current implementation.

setRandomSeed(long) - Method in class htsjdk.samtools.SAMRecordSetBuilder

Set the seed of the random number generator for cases in which repeatable result is desired.

setRawContent(byte[]) - Method in class htsjdk.samtools.cram.structure.Block
 
setReadBases(byte[]) - Method in class htsjdk.samtools.BAMRecord
 
setReadBases(byte[]) - Method in class htsjdk.samtools.SAMRecord
 
setReadBases(byte[]) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setReadFailsVendorQualityCheckFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the read fails platform/vendor quality checks.

setReadGroup(SAMReadGroupRecord) - Method in class htsjdk.samtools.SAMRecordSetBuilder
 
setReadGroups(List<SAMReadGroupRecord>) - Method in class htsjdk.samtools.SAMFileHeader

Replace entire list of read groups.

setReadingFrame(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon

Method description

setReadingFrame(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Method description

setReadLength(int) - Method in class htsjdk.samtools.SAMRecordSetBuilder
 
setReadName(String) - Method in class htsjdk.samtools.BAMRecord
 
setReadName(String) - Method in class htsjdk.samtools.SAMRecord
 
setReadNegativeStrandFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

strand of the query (false for forward; true for reverse strand).

setReadNegativeStrandFlag(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setReadPairedFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the read is paired in sequencing, no matter whether it is mapped in a pair.

setReadPairedFlag(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setReadString(String) - Method in class htsjdk.samtools.SAMRecord
 
setReadUmappedFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

Deprecated. 

setReadUnmappedFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the query sequence itself is unmapped.

setRecord(SAMRecord) - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
 
setRecordBytes(byte[]) - Method in class htsjdk.variant.bcf2.BCF2Decoder

Use the recordBytes[] to read BCF2 records from now on

setRecordNumber(long) - Method in class htsjdk.samtools.SAMValidationError
 
setRecordOrdinal(long) - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
 
setRefBases(byte[]) - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
setReferenceBase(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
setReferenceDictionary(SAMSequenceDictionary) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Set the reference dictionary to be used by VariantContextWriters created by this builder.

setReferenceIndex(int) - Method in class htsjdk.samtools.SAMRecord

Updates the reference index.

setReferenceIndex(int) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setReferenceName(String) - Method in class htsjdk.samtools.SAMRecord

Sets the reference name for this record.

setReferenceName(String) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setRefMD5(byte[]) - Method in class htsjdk.samtools.cram.structure.Slice
 
setRefSNPs(byte[]) - Method in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
setRemappedSampleName(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec

Replaces the sample name read from the VCF header with the remappedSampleName.

setRestPosition(long) - Method in class htsjdk.samtools.util.ftp.FTPClient
 
setResultState(SamRecordWithOrdinal, boolean) - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer

Mark the current samRecordWithOrdinal as having been examined.

setResultState(boolean) - Method in class htsjdk.samtools.util.SamRecordWithOrdinal

Set the result state on this record.

setRunDate(Date) - Method in class htsjdk.samtools.SAMReadGroupRecord

Converts to Iso8601Date if not already in that form.

setSamFilters(List<SamRecordFilter>) - Method in class htsjdk.samtools.util.AbstractLocusIterator

Controls which, if any, SAMRecords are filtered.

setSamFlagFieldOutput(SamFlagField) - Method in class htsjdk.samtools.SAMFileWriterFactory

Set the flag output format only when writing text.

setSample(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setScore(float) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setScores(byte[]) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy) - Method in class htsjdk.samtools.DuplicateSetIterator

Deprecated.

setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy) - Method in class htsjdk.samtools.SAMRecordDuplicateComparator
 
setSecondaryAlignment(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setSecondOfPairFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the read is the second read in a pair.

setSecondOfPairFlag(boolean) - Method in class htsjdk.samtools.sra.SRALazyRecord
 
setSeconds(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

setSegmentUnmapped(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setSentinel(V) - Method in class htsjdk.samtools.util.IntervalTree

Set the special sentinel value that will be used to signal novelty when putting a new interval
 into the tree, or to signal "not found" when removing an interval.

setSequence(byte[]) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
setSequence(byte[]) - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
setSequenceDictionary(SAMSequenceDictionary) - Method in class htsjdk.samtools.SAMFileHeader

Replace entire sequence dictionary.

setSequenceDictionary(SAMSequenceDictionary) - Method in class htsjdk.variant.vcf.VCFHeader

Completely replaces the contig records in this header with those in the given SAMSequenceDictionary.

setSequenceIndex(int) - Method in class htsjdk.samtools.SAMSequenceRecord
 
setSequenceLength(int) - Method in class htsjdk.samtools.SAMSequenceRecord
 
setSequences(List<SAMSequenceRecord>) - Method in class htsjdk.samtools.SAMSequenceDictionary

Replaces the existing list of SAMSequenceRecords with the given list.

setSequencingCenter(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
 
setSortOrder(SAMFileHeader.SortOrder) - Method in class htsjdk.samtools.SAMFileHeader
 
setSortOrder(SAMFileHeader.SortOrder, boolean) - Method in class htsjdk.samtools.SAMFileWriterImpl

Must be called before calling setHeader().

setSource(String) - Method in class htsjdk.samtools.SAMValidationError
 
setSource(String) - Method in exception htsjdk.tribble.TribbleException

set the source for the file; where we got lines from

setSpan(int) - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
 
setSpecies(String) - Method in class htsjdk.samtools.SAMSequenceRecord
 
setStart(int) - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
 
setStart(int) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setStrand(Strand) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setSupplementary(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setSupplementaryAlignmentFlag(boolean) - Method in class htsjdk.samtools.SAMRecord

the alignment is supplementary (TODO: further explanation?).

setTempDirectory(File) - Method in class htsjdk.samtools.SAMFileWriterFactory

Set the temporary directory to use when sort data.

setTextHeader(String) - Method in class htsjdk.samtools.SAMFileHeader
 
setTime(long) - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

setTransientAttribute(Object, Object) - Method in class htsjdk.samtools.SAMRecord

Sets the value of a transient attribute, and returns the previous value if defined.

setTS(long) - Method in class htsjdk.tribble.index.linear.LinearIndex
 
setType(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
 
setUnknownBases(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setUnmappedHasBasesAndQualities(boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder
 
setUnsignedArrayAttribute(String, Object) - Method in class htsjdk.samtools.cram.structure.Slice
 
setUnsignedArrayAttribute(String, Object) - Method in class htsjdk.samtools.SAMRecord

Because Java does not support unsigned integer types, we think it is a bad idea to encode them in SAM
 files.

setup(VCFHeader, BCF2Encoder, Map<String, Integer>) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager

Setup the FieldWriters appropriate to each INFO and FORMAT in the VCF header

 Must be called before any of the getter methods will work

setUseAsyncIo(boolean) - Method in class htsjdk.samtools.fastq.FastqWriterFactory

Sets whether or not to use async io (i.e.

setUseAsyncIo(boolean) - Method in class htsjdk.samtools.SAMFileWriterFactory

Turn on or off the use of asynchronous IO for writing output SAM and BAM files.

setUseAsyncIo(boolean) - Method in class htsjdk.samtools.SamReaderFactory

Set whether readers created by this factory will use asynchronous IO.

setUseNmFlag(boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder
 
setUTR(boolean) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon

Flag indicating that the entire exon is the UTR.

setUTR(boolean) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2

Flag indicating that the entire exon is the UTR.

setValidateIndex(boolean) - Method in class htsjdk.samtools.SamFileValidator

Deprecated.
use SamFileValidator.setIndexValidationStringency(htsjdk.samtools.BamIndexValidator.IndexValidationStringency) instead


setValidationErrors(Collection<SAMValidationError>) - Method in class htsjdk.samtools.SAMFileHeader

Replace list of validation errors with the elements of the given list.

setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.CRAMIterator
 
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.SAMRecord

Control validation of lazily-decoded elements.

setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec
 
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.SAMTextHeaderCodec
 
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.sra.SRAAlignmentIterator
 
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.sra.SRAUnalignmentIterator
 
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.SRAIterator
 
setValue(String) - Method in class htsjdk.samtools.metrics.StringHeader
 
setValue(V1) - Method in class htsjdk.samtools.util.IntervalTree.Node
 
setValueLabel(String) - Method in class htsjdk.samtools.util.Histogram
 
setVCFHeader(VCFHeader, VCFHeaderVersion) - Method in class htsjdk.variant.vcf.AbstractVCFCodec

Explicitly set the VCFHeader on this codec.

setVCFHeader(VCFHeader) - Method in class htsjdk.variant.vcf.VCFEncoder

Deprecated.

setVendorFiltered(boolean) - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
setVerbose(boolean, int) - Method in class htsjdk.samtools.SamFileValidator

Control verbosity

setVersion(Version) - Method in class htsjdk.samtools.cram.structure.CramHeader
 
setVersionedItem(String) - Method in class htsjdk.samtools.metrics.VersionHeader
 
setVersionString(String) - Method in class htsjdk.samtools.metrics.VersionHeader
 
setWriteCommandLine(boolean) - Method in class htsjdk.variant.vcf.VCFHeader

If true, and isWriteEngineHeaders also returns true, the command line will be written to the VCF.

setWriteEngineHeaders(boolean) - Method in class htsjdk.variant.vcf.VCFHeader

If true additional engine headers will be written to the VCF, otherwise only the walker headers will be output.

setWrittenCount(long) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
setYear(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date

Deprecated.

severity - Variable in enum htsjdk.samtools.SAMValidationError.Type
 
shadowBCF(File) - Static method in class htsjdk.variant.bcf2.BCF2Utils

Returns a good name for a shadow BCF file for vcfFile.

shouldBeAddedToDictionary() - Method in class htsjdk.variant.vcf.VCFFilterHeaderLine
 
shouldBeAddedToDictionary() - Method in class htsjdk.variant.vcf.VCFFormatHeaderLine
 
shouldBeAddedToDictionary() - Method in class htsjdk.variant.vcf.VCFHeaderLine

By default the header lines won't be added to the dictionary, unless this method will be override (for example in FORMAT, INFO or FILTER header lines)

shouldBeAddedToDictionary() - Method in class htsjdk.variant.vcf.VCFInfoHeaderLine
 
shouldFlushContainer(SAMRecord) - Method in class htsjdk.samtools.CRAMContainerStreamWriter

Decide if the current container should be completed and flushed.

showDialog() - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
 
SimpleBEDFeature - Class in htsjdk.tribble.bed

Feature from a BED file without exon blocks.

SimpleBEDFeature(int, int, String) - Constructor for class htsjdk.tribble.bed.SimpleBEDFeature
 
SimpleFeature - Class in htsjdk.tribble

A simple concrete Feature.

SimpleFeature(String, int, int) - Constructor for class htsjdk.tribble.SimpleFeature
 
site(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenericSiteWriter
 
site(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.SiteWriter
 
sitesOnlyVariantContext(VariantContext) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Returns a newly allocated VC that is the same as VC, but without genotypes

sitesOnlyVariantContexts(Collection<VariantContext>) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils

Returns a newly allocated list of VC, where each VC is the same as the input VCs, but without genotypes

SiteWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.SiteWriter
 
size() - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap
 
size() - Method in class htsjdk.samtools.cram.common.IntHashMap


 Returns the number of keys in this hashtable.

size - Variable in class htsjdk.samtools.cram.structure.Slice
 
size() - Method in class htsjdk.samtools.DuplicateSet

Returns the number of records in this set.

size() - Method in class htsjdk.samtools.LinearIndex
 
size() - Method in class htsjdk.samtools.reference.FastaSequenceIndex

Returns the number of elements in the index.

size() - Method in class htsjdk.samtools.SAMRecordSetBuilder
 
size() - Method in class htsjdk.samtools.SAMSequenceDictionary
 
size() - Method in class htsjdk.samtools.util.AbstractLocusInfo
 
size() - Method in class htsjdk.samtools.util.DiskBackedQueue

Return the total number of elements in the queue, both in memory and on disk

size(String) - Method in class htsjdk.samtools.util.ftp.FTPClient

Return the size of the remote file

size() - Method in class htsjdk.samtools.util.Histogram

Returns the size of this histogram.

size() - Method in class htsjdk.samtools.util.IntervalList

Returns the count of intervals in the list.

size() - Method in class htsjdk.samtools.util.IntervalTree

Return the number of intervals in the tree.

size() - Method in class htsjdk.samtools.util.IntervalTreeMap
 
size() - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
 
size() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer

Return the total number of elements in the queue, both in memory and on disk

size() - Method in class htsjdk.tribble.index.interval.IntervalTree
 
size() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
size() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
 
sizeInRam() - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap
 
sizeIsOverflow(byte) - Static method in class htsjdk.variant.bcf2.BCF2Utils
 
SIZEOF - Static variable in class htsjdk.samtools.util.SortingLongCollection
 
sizeOfTree(File) - Static method in class htsjdk.samtools.util.IOUtil

Returns the size (in bytes) of the file or directory and all it's children.

skip(BitInputStream) - Method in class htsjdk.samtools.cram.encoding.AbstractBitCodec
 
skip(BitInputStream, int) - Method in class htsjdk.samtools.cram.encoding.AbstractBitCodec
 
skip(BitInputStream) - Method in interface htsjdk.samtools.cram.encoding.BitCodec

Skip the next object in the bit stream.

skip(BitInputStream, int) - Method in interface htsjdk.samtools.cram.encoding.BitCodec

Skip the next length objects in the bit stream.

skip(long) - Method in class htsjdk.samtools.cram.io.CountingInputStream
 
skip(long) - Method in class htsjdk.samtools.cram.io.CRC32InputStream
 
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
 
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
 
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
 
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
 
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
 
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
 
skip(long) - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
 
skip(long) - Method in class htsjdk.tribble.readers.LongLineBufferedReader

Skips characters.

skip(long) - Method in interface htsjdk.tribble.readers.Positional

Skip the next nBytes in the stream.

skip(long) - Method in class htsjdk.tribble.readers.PositionalBufferedStream
 
skipHeaderBytes() - Method in class htsjdk.tribble.FeatureCodecHeader
 
skipNewlines() - Method in class htsjdk.samtools.util.FastLineReader

Advance over any EOLN chars (CR or LF)

skipNextBlock(int, InputStream) - Method in class htsjdk.variant.bcf2.BCF2Decoder

Skips the next record from input stream, invalidating current block data

SKIPPED_REGION - Static variable in enum htsjdk.samtools.CigarOperator
 
Slice - Class in htsjdk.samtools.cram.structure

CRAM slice is a logical union of blocks into for example alignment slices.

Slice() - Constructor for class htsjdk.samtools.cram.structure.Slice
 
sliceIndex - Variable in class htsjdk.samtools.cram.CRAIEntry
 
sliceIndex - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
sliceOffset - Variable in class htsjdk.samtools.cram.CRAIEntry
 
slices - Variable in class htsjdk.samtools.cram.structure.Container
 
sliceSize - Variable in class htsjdk.samtools.cram.CRAIEntry
 
sliceTags - Variable in class htsjdk.samtools.cram.structure.Slice
 
slurp(File) - Static method in class htsjdk.samtools.util.IOUtil

Convenience overload for IOUtil.slurp(java.io.InputStream, java.nio.charset.Charset) using the default charset Charset.defaultCharset().

slurp(InputStream) - Static method in class htsjdk.samtools.util.IOUtil

Convenience overload for IOUtil.slurp(java.io.InputStream, java.nio.charset.Charset) using the default charset Charset.defaultCharset().

slurp(InputStream, Charset) - Static method in class htsjdk.samtools.util.IOUtil

Reads all of the stream into a String, decoding with the provided Charset then closes the stream quietly.

slurp(Iterator<T>) - Static method in class htsjdk.samtools.util.Iterables
 
slurp(Iterable<T>) - Static method in class htsjdk.samtools.util.Iterables
 
slurpLines(File) - Static method in class htsjdk.samtools.util.IOUtil

Returns all of the untrimmed lines in the provided file.

slurpLines(InputStream) - Static method in class htsjdk.samtools.util.IOUtil
 
SM - Variable in class htsjdk.samtools.SAMTagUtil
 
smartMergeHeaders(Collection<VCFHeader>, boolean) - Static method in class htsjdk.variant.vcf.VCFUtils
 
SnappyAvailable - Variable in class htsjdk.samtools.util.SnappyLoader
 
SnappyLoader - Class in htsjdk.samtools.util

If Snappy is available, obtain single-arg ctors for SnappyInputStream and SnappyOutputStream.

SnappyLoader() - Constructor for class htsjdk.samtools.util.SnappyLoader
 
SnappyLoader(boolean) - Constructor for class htsjdk.samtools.util.SnappyLoader

Constructs a new SnappyLoader which will check to see if snappy is available in the JVM/library path.

SnpFilter - Class in htsjdk.variant.variantcontext.filter

A Predicate on VariantContexts that  returns true at sites that are SNPs

SnpFilter() - Constructor for class htsjdk.variant.variantcontext.filter.SnpFilter
 
SOFT_CLIP - Static variable in enum htsjdk.samtools.CigarOperator
 
SoftClip - Class in htsjdk.samtools.cram.encoding.readfeatures

A read feature representing a soft clip similar to CigarOperator.S.

SoftClip() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
SoftClip(int, byte[]) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
softClip3PrimeEndOfRead(SAMRecord, int) - Static method in class htsjdk.samtools.util.CigarUtil

Adds a soft-clip, based on clipFrom, to the SAM record's existing cigar
 and, for negative strands, also adjusts the SAM record's start position.

softClipCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
softClipCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
softClipEndOfRead(int, List<CigarElement>) - Static method in class htsjdk.samtools.util.CigarUtil

adjust the cigar based on adapter clipping.

SOLEXA_ADDEND - Static variable in class htsjdk.samtools.util.SolexaQualityConverter

This value is added to a Solexa quality score to make it printable ASCII

solexaCharToPhredBinary(byte) - Method in class htsjdk.samtools.util.SolexaQualityConverter

Convert a solexa quality ASCII character into a phred score.

SolexaNoiseFilter - Class in htsjdk.samtools.filter

Filter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact.

SolexaNoiseFilter() - Constructor for class htsjdk.samtools.filter.SolexaNoiseFilter
 
SolexaQualityConverter - Class in htsjdk.samtools.util

Optimized method for converting Solexa ASCII qualities into Phred scores.

SOMATIC_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
sort() - Method in class htsjdk.samtools.util.IntervalList

Deprecated.
use IntervalList.sorted() instead.


SORT_ORDER_TAG - Static variable in class htsjdk.samtools.SAMFileHeader
 
sorted() - Method in class htsjdk.samtools.util.IntervalList

returns an independent sorted IntervalList

sortedString(Map<T, V>) - Static method in class htsjdk.tribble.util.ParsingUtils
 
sortedString(Map<T, V>) - Static method in class htsjdk.variant.variantcontext.Genotype

a utility method for generating sorted strings from a map key set.

SortingCollection<T> - Class in htsjdk.samtools.util

Collection to which many records can be added.

SortingCollection.Codec<T> - Interface in htsjdk.samtools.util

Client must implement this class, which defines the way in which records are written to and
 read from file.

SortingLongCollection - Class in htsjdk.samtools.util

Accumulate a list of longs that can then be sorted in natural order and iterated over.

SortingLongCollection(int, File...) - Constructor for class htsjdk.samtools.util.SortingLongCollection

Prepare to accumulate values to be sorted

SortingVariantContextWriter - Class in htsjdk.variant.variantcontext.writer

this class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away)

SortingVariantContextWriter(VariantContextWriter, int, boolean) - Constructor for class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter

create a local-sorting VCF writer, given an inner VCF writer to write to

SortingVariantContextWriter(VariantContextWriter, int) - Constructor for class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
 
sortList(Collection<T>) - Static method in class htsjdk.tribble.util.ParsingUtils

a small utility function for sorting a list

sortOnTheFly(VariantContextWriter, int) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.
 
sortOnTheFly(VariantContextWriter, int, boolean) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.
 
source(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells us that the resulting VariantContext should have source field set to source

SOURCE_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
 
sourceLikeBam(SeekableStream) - Static method in class htsjdk.samtools.SamStreams
 
sourceLikeCram(SeekableStream) - Static method in class htsjdk.samtools.SamStreams
 
SPAN_DEL - Static variable in class htsjdk.variant.variantcontext.Allele
 
SPAN_DEL_STRING - Static variable in class htsjdk.variant.variantcontext.Allele

A generic static SPAN_DEL allele for use

SPANNING_DELETION_ALLELE - Static variable in class htsjdk.variant.vcf.VCFConstants
 
SPECIES_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
 
split(String, String[], char) - Static method in class htsjdk.samtools.util.StringUtil

Split the string into tokens separated by the given delimiter.

split(String, char) - Static method in class htsjdk.tribble.util.ParsingUtils

Split the string into tokens separated by the given delimiter.

split(String, String[], char) - Static method in class htsjdk.tribble.util.ParsingUtils

Split the string into tokesn separated by the given delimiter.

split(String, String[], char, boolean) - Static method in class htsjdk.tribble.util.ParsingUtils

Split the string into tokens separated by the given delimiter.

splitConcatenateExcessTokens(String, String[], char) - Static method in class htsjdk.samtools.util.StringUtil

Split the string into tokens separated by the given delimiter.

splitWhitespace(String, String[]) - Static method in class htsjdk.tribble.util.ParsingUtils

Split the string into tokens separated by tab or space(s).

SQ - Variable in class htsjdk.samtools.SAMTagUtil
 
sqScaledProbabilityRatio(double, double) - Static method in class htsjdk.samtools.SQTagUtil

Convert a pair of likelihoods into a value suitable for passing to baseAndProbDiffToSqValue.

SQTagUtil - Class in htsjdk.samtools

Utility methods for encoding and decoding the SQ tag value of SAMRecord.

SQTagUtil() - Constructor for class htsjdk.samtools.SQTagUtil
 
SQTagUtil.SQBase - Enum in htsjdk.samtools

The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag.

sqValueToBase(byte) - Static method in class htsjdk.samtools.SQTagUtil

Retrieve the 2nd-best base call from SQ value.

sqValueToBaseOrdinal(byte) - Static method in class htsjdk.samtools.SQTagUtil

Retrieve the 2nd-best base call from SQ value.

sqValueToProbRatio(byte) - Static method in class htsjdk.samtools.SQTagUtil

Retrieve SQ-scaled probability ratio from SQ value.

SRA_BIN_SIZE - Static variable in class htsjdk.samtools.SRAIndex

Number of reference bases bins in last level can represent

SRA_CHUNK_SIZE - Static variable in class htsjdk.samtools.SRAIndex

Chunks of that size will be created when using SRA index

SRA_LIBRARIES_DOWNLOAD - Static variable in class htsjdk.samtools.Defaults

Boolean describing whether downloading of SRA native libraries is allowed,
 in case such native libraries are not found locally

SRA_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
 
SRAAccession - Class in htsjdk.samtools.sra

Describes a single SRA accession for SRA read collection
 Also provides app string functionality and allows to check if working SRA is supported on the running platform

 Important: due to checks performed in SRAAccession.isValid(), we won't recognise any accessions other
 than ones that follow the pattern "^[SED]RR[0-9]{6,9}$", e.g.

SRAAccession(String) - Constructor for class htsjdk.samtools.sra.SRAAccession
 
SRAAlignmentIterator - Class in htsjdk.samtools.sra

Iterator for aligned reads.

SRAAlignmentIterator(SRAAccession, ReadCollection, SAMFileHeader, ReferenceCache, SRAIterator.RecordRangeInfo, Chunk) - Constructor for class htsjdk.samtools.sra.SRAAlignmentIterator
 
SRAFileReader - Class in htsjdk.samtools
 
SRAFileReader(SRAAccession) - Constructor for class htsjdk.samtools.SRAFileReader
 
SRAIndex - Class in htsjdk.samtools

Emulates BAM index so that we can request chunks of records from SRAFileReader

 Here is how it works:
  SRA allows reading of alignments by Reference position fast, so we divide our "file" range for alignments as
  a length of all references.

SRAIndex(SAMFileHeader, SRAIterator.RecordRangeInfo) - Constructor for class htsjdk.samtools.SRAIndex
 
SRAIndexedSequenceFile - Class in htsjdk.samtools.sra

Allows reading Reference data from SRA

SRAIndexedSequenceFile(SRAAccession) - Constructor for class htsjdk.samtools.sra.SRAIndexedSequenceFile
 
SRAIterator - Class in htsjdk.samtools

SRA iterator which returns SAMRecords for requested list of chunks

SRAIterator(SRAAccession, ReadCollection, SAMFileHeader, ReferenceCache, SRAIterator.RecordRangeInfo, List<Chunk>) - Constructor for class htsjdk.samtools.SRAIterator
 
SRAIterator.RecordRangeInfo - Class in htsjdk.samtools

Describes record ranges info needed for emulating BAM index

SRALazyRecord - Class in htsjdk.samtools.sra

Extends SAMRecord so that any of the fields will be loaded only when needed.

SRALazyRecord(SAMFileHeader, SRAAccession, ReadCollection, AlignmentIterator, String, String) - Constructor for class htsjdk.samtools.sra.SRALazyRecord
 
SRALazyRecord(SAMFileHeader, SRAAccession, ReadCollection, ReadIterator, String, int) - Constructor for class htsjdk.samtools.sra.SRALazyRecord
 
SRALazyRecord(SAMFileHeader, SRAAccession, String, String) - Constructor for class htsjdk.samtools.sra.SRALazyRecord
 
SRALazyRecord(SAMFileHeader, SRAAccession, String, int) - Constructor for class htsjdk.samtools.sra.SRALazyRecord
 
SRAUnalignmentIterator - Class in htsjdk.samtools.sra

Iterator for unaligned reads.

SRAUnalignmentIterator(SRAAccession, ReadCollection, SAMFileHeader, SRAIterator.RecordRangeInfo, Chunk) - Constructor for class htsjdk.samtools.sra.SRAUnalignmentIterator
 
SRAUtils - Class in htsjdk.samtools.sra

Provides some functionality which can be used by other classes

 Created by andrii.nikitiuk on 10/28/15.

SRAUtils() - Constructor for class htsjdk.samtools.sra.SRAUtils
 
STANDARD_BUFFER_SIZE - Static variable in class htsjdk.samtools.util.IOUtil

Deprecated.
Use Defaults.NON_ZERO_BUFFER_SIZE instead.


STANDARD_INDEX_EXTENSION - Static variable in class htsjdk.tribble.Tribble
 
STANDARD_INDEX_EXTENSION - Static variable in class htsjdk.tribble.util.TabixUtils
 
STANDARD_TAGS - Static variable in class htsjdk.samtools.SAMFileHeader

These tags are of known type, so don't need a type field in the text representation.

STANDARD_TAGS - Static variable in class htsjdk.samtools.SAMProgramRecord
 
STANDARD_TAGS - Static variable in class htsjdk.samtools.SAMReadGroupRecord
 
STANDARD_TAGS - Static variable in class htsjdk.samtools.SAMSequenceRecord

The standard tags are stored in text header without type information, because the type of these tags is known.

standardDeviation() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
 
start - Variable in class htsjdk.samtools.QueryInterval

1-based, inclusive

start() - Method in class htsjdk.samtools.util.StopWatch
 
start - Variable in class htsjdk.tribble.bed.SimpleBEDFeature
 
start - Variable in class htsjdk.variant.variantcontext.VariantContext
 
start(long) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells us that the resulting VariantContext should have the specified contig start

start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
 
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GTWriter
 
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
 
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IntegerTypeGenotypesWriter
 
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
 
startPositionColumn - Variable in class htsjdk.tribble.index.tabix.TabixFormat

One-based index of the column in the file being indexed containing the start position.

startWithInsertion(Cigar) - Static method in class htsjdk.samtools.util.AbstractLocusIterator

Check if cigar start with an insertion, ignoring other operators that do not consume references bases

StaticallyTypeGenotypesWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.StaticallyTypeGenotypesWriter
 
statsSummary() - Method in class htsjdk.tribble.index.AbstractIndex
 
stderr - Variable in class htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput

May be null if interleaved

stdout - Variable in class htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
 
stop() - Method in class htsjdk.samtools.util.StopWatch
 
stop - Variable in class htsjdk.variant.variantcontext.VariantContext
 
stop(long) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells us that the resulting VariantContext should have the specified contig stop

StopWatch - Class in htsjdk.samtools.util

Utility to help in performance testing.

StopWatch() - Constructor for class htsjdk.samtools.util.StopWatch
 
Strand - Enum in htsjdk.tribble.annotation

Enum for strand, which can be encoded as string

strand - Variable in class htsjdk.tribble.bed.SimpleBEDFeature
 
STRAND_BIAS_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
stream() - Method in interface htsjdk.samtools.util.CloseableIterator

Returns a Stream that will consume from the underlying iterator.

STREAM_TYPES - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
 
stringCache - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
StringHeader - Class in htsjdk.samtools.metrics

A simple header who's data type is a single String.

StringHeader() - Constructor for class htsjdk.samtools.metrics.StringHeader

Default constructor.

StringHeader(String) - Constructor for class htsjdk.samtools.metrics.StringHeader

Constructor that uses the supplied value as the value of the header.

StringLineReader - Class in htsjdk.samtools.util

Implementation of LineReader that gets its input from a String.

StringLineReader(String) - Constructor for class htsjdk.samtools.util.StringLineReader
 
StringOrCharacter(VCFCompoundHeaderLine, Map<String, Integer>) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
 
stringToBytes(String) - Static method in class htsjdk.samtools.util.StringUtil
 
stringToBytes(String, int, int) - Static method in class htsjdk.samtools.util.StringUtil
 
StringUtil - Class in htsjdk.samtools.util

Grab-bag of stateless String-oriented utilities.

StringUtil() - Constructor for class htsjdk.samtools.util.StringUtil
 
StructuralVariantType - Enum in htsjdk.variant.variantcontext

Type of Structural Variant as defined in the VCF spec 4.2

subContextFromSample(String) - Method in class htsjdk.variant.variantcontext.VariantContext
 
subContextFromSamples(Set<String>, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext

This method subsets down to a set of samples.

subContextFromSamples(Set<String>) - Method in class htsjdk.variant.variantcontext.VariantContext
 
SubexponentialIntegerEncoding - Class in htsjdk.samtools.cram.encoding
 
SubexponentialIntegerEncoding() - Constructor for class htsjdk.samtools.cram.encoding.SubexponentialIntegerEncoding
 
SubexponentialIntegerEncoding(int, int) - Constructor for class htsjdk.samtools.cram.encoding.SubexponentialIntegerEncoding
 
subList(int, int) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
subsetToSamples(Set<String>) - Method in class htsjdk.variant.variantcontext.GenotypesContext

Return a freshly allocated subcontext of this context containing only the samples
 listed in samples.

Substitution - Class in htsjdk.samtools.cram.encoding.readfeatures

A substitution event captured in read coordinates.

Substitution() - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
substitutionMatrix - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
substitutionMatrix - Variable in class htsjdk.samtools.cram.structure.CompressionHeader
 
SubstitutionMatrix - Class in htsjdk.samtools.cram.structure
 
SubstitutionMatrix(long[][]) - Constructor for class htsjdk.samtools.cram.structure.SubstitutionMatrix
 
SubstitutionMatrix(byte[]) - Constructor for class htsjdk.samtools.cram.structure.SubstitutionMatrix
 
subtract(Collection<IntervalList>, Collection<IntervalList>) - Static method in class htsjdk.samtools.util.IntervalList

A utility function for subtracting a collection of IntervalLists from another.

subtract(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList

A utility function for subtracting a single IntervalList from another.

sumOfErrorProbabilities(SAMRecord) - Static method in class htsjdk.samtools.util.QualityUtil

Calculates the sum of error probabilities for all read bases in the SAM record.

sumQualitiesOfMismatches(SAMRecord, byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil

Calculates the sum of qualities for mismatched bases in the read.

sumQualitiesOfMismatches(SAMRecord, byte[], int) - Static method in class htsjdk.samtools.util.SequenceUtil

Calculates the sum of qualities for mismatched bases in the read.

sumQualitiesOfMismatches(SAMRecord, byte[], int, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil

Calculates the sum of qualities for mismatched bases in the read.

SUPPLEMENTARY_FLAG - Static variable in class htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
 
SVTYPE - Static variable in class htsjdk.variant.vcf.VCFConstants

INFO Type of structural variant

SynchronousLineReader - Class in htsjdk.tribble.readers

Implementation of LineReader that reads lines directly from the underlying stream or reader.

SynchronousLineReader(InputStream) - Constructor for class htsjdk.tribble.readers.SynchronousLineReader
 
SynchronousLineReader(Reader) - Constructor for class htsjdk.tribble.readers.SynchronousLineReader
 
synchronouslyClose() - Method in class htsjdk.samtools.fastq.AsyncFastqWriter
 
synchronouslyClose() - Method in class htsjdk.samtools.util.AbstractAsyncWriter
 
synchronouslyClose() - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
 
synchronouslyWrite(FastqRecord) - Method in class htsjdk.samtools.fastq.AsyncFastqWriter
 
synchronouslyWrite(T) - Method in class htsjdk.samtools.util.AbstractAsyncWriter
 
synchronouslyWrite(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
 




T

t - Static variable in class htsjdk.samtools.util.SequenceUtil

Byte typed variables for all normal bases.

T - Static variable in class htsjdk.samtools.util.SequenceUtil

Byte typed variables for all normal bases.

TabixFeatureReader<T extends Feature,SOURCE> - Class in htsjdk.tribble
 
TabixFeatureReader(String, AsciiFeatureCodec) - Constructor for class htsjdk.tribble.TabixFeatureReader
 
TabixFeatureReader(String, String, AsciiFeatureCodec) - Constructor for class htsjdk.tribble.TabixFeatureReader
 
TabixFormat - Class in htsjdk.tribble.index.tabix

The values in a Tabix header that define the format of the file being indexed, e.g.

TabixFormat() - Constructor for class htsjdk.tribble.index.tabix.TabixFormat
 
TabixFormat(int, int, int, int, char, int) - Constructor for class htsjdk.tribble.index.tabix.TabixFormat
 
TabixIndex - Class in htsjdk.tribble.index.tabix

This class represent a Tabix index that has been built in memory or read from a file.

TabixIndex(TabixFormat, List<String>, BinningIndexContent[]) - Constructor for class htsjdk.tribble.index.tabix.TabixIndex
 
TabixIndex(InputStream) - Constructor for class htsjdk.tribble.index.tabix.TabixIndex
 
TabixIndex(File) - Constructor for class htsjdk.tribble.index.tabix.TabixIndex

Convenient ctor that opens the file, wraps with with BGZF reader, and closes after reading index.

TabixIndexCreator - Class in htsjdk.tribble.index.tabix

IndexCreator for Tabix.

TabixIndexCreator(SAMSequenceDictionary, TabixFormat) - Constructor for class htsjdk.tribble.index.tabix.TabixIndexCreator
 
TabixIndexCreator(TabixFormat) - Constructor for class htsjdk.tribble.index.tabix.TabixIndexCreator
 
tabixIndexFile(String) - Static method in class htsjdk.tribble.Tribble

Return the name of the tabix index file for the provided vcf filename
 Does not actually create an index

tabixIndexFile(File) - Static method in class htsjdk.tribble.Tribble

Return the File of the tabix index file for the provided vcf file
 Does not actually create an index

TabixIteratorLineReader - Class in htsjdk.tribble.readers
 
TabixIteratorLineReader(TabixReader.Iterator) - Constructor for class htsjdk.tribble.readers.TabixIteratorLineReader
 
TabixReader - Class in htsjdk.tribble.readers
 
TabixReader(String) - Constructor for class htsjdk.tribble.readers.TabixReader
 
TabixReader(String, String) - Constructor for class htsjdk.tribble.readers.TabixReader
 
TabixReader(String, SeekableStream) - Constructor for class htsjdk.tribble.readers.TabixReader
 
TabixReader(String, String, SeekableStream) - Constructor for class htsjdk.tribble.readers.TabixReader
 
TabixReader.Iterator - Interface in htsjdk.tribble.readers
 
TabixReader.TIndex - Class in htsjdk.tribble.readers
 
TabixReader.TPair64 - Class in htsjdk.tribble.readers
 
TabixReaderFailure(String, String, Exception) - Constructor for exception htsjdk.tribble.TribbleException.TabixReaderFailure
 
TabixReaderFailure(String, String) - Constructor for exception htsjdk.tribble.TribbleException.TabixReaderFailure
 
TabixUtils - Class in htsjdk.tribble.util

classes that have anything to do with tabix

TabixUtils() - Constructor for class htsjdk.tribble.util.TabixUtils
 
TabixUtils.TIndex - Class in htsjdk.tribble.util
 
TabixUtils.TIntv - Class in htsjdk.tribble.util
 
TabixUtils.TPair64 - Class in htsjdk.tribble.util
 
tag - Variable in class htsjdk.samtools.SAMBinaryTagAndValue
 
tag - Variable in class htsjdk.samtools.SAMRecord.SAMTagAndValue
 
TagFilter - Class in htsjdk.samtools.filter

Filter class for matching tag attributes in SAMRecords

 $Id$

TagFilter(String, Object) - Constructor for class htsjdk.samtools.filter.TagFilter

Constructor for a single value

TagFilter(String, List<Object>) - Constructor for class htsjdk.samtools.filter.TagFilter

Constructor for multiple values

tagIdDictionary - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
tagIdListCodec - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
tagIdListCodec - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
tagIds - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
tagIdsIndex - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
tags - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
TAGS_TO_REVERSE - Static variable in class htsjdk.samtools.SAMRecord

Tags that are known to need the reverse if the read is reverse complemented.

TAGS_TO_REVERSE - Static variable in class htsjdk.samtools.SAMRecordUtil

Deprecated.
 
TAGS_TO_REVERSE_COMPLEMENT - Static variable in class htsjdk.samtools.SAMRecord

Tags that are known to need the reverse complement if the read is reverse complemented.

TAGS_TO_REVERSE_COMPLEMENT - Static variable in class htsjdk.samtools.SAMRecordUtil

Deprecated.
 
TagValueAndUnsignedArrayFlag - Class in htsjdk.samtools

CVO to use as a method return value.

TagValueAndUnsignedArrayFlag(Object, boolean) - Constructor for class htsjdk.samtools.TagValueAndUnsignedArrayFlag
 
tagValueCodecs - Variable in class htsjdk.samtools.cram.encoding.reader.AbstractReader
 
tagValueCodecs - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
templateSize - Variable in class htsjdk.samtools.cram.encoding.writer.Writer
 
templateSize - Variable in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
TempStreamFactory - Class in htsjdk.samtools.util

Factory class for wrapping input and output streams for temporary files.

TempStreamFactory() - Constructor for class htsjdk.samtools.util.TempStreamFactory
 
test(SAMBinaryTagAndValue) - Method in class htsjdk.samtools.cram.digest.ContentDigests
 
test(String) - Static method in class htsjdk.samtools.util.DateParser
 
test(Date) - Static method in class htsjdk.samtools.util.DateParser
 
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.CompoundFilter
 
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.GenotypeQualityFilter
 
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.HeterozygosityFilter
 
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter

Determines whether a VariantContext matches this filter

test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.PassingVariantFilter
 
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.SnpFilter
 
test(VariantContext) - Method in interface htsjdk.variant.variantcontext.filter.VariantContextFilter

Determines whether a VariantContext matches this filter

TestUtil - Class in htsjdk.samtools.util
 
TestUtil() - Constructor for class htsjdk.samtools.util.TestUtil
 
TextCigarCodec - Class in htsjdk.samtools

Convert between String and Cigar class representations of CIGAR.

TextCigarCodec() - Constructor for class htsjdk.samtools.TextCigarCodec
 
TextTagCodec - Class in htsjdk.samtools

Converter between SAM text representation of a tag, and in-memory Object representation.

TextTagCodec() - Constructor for class htsjdk.samtools.TextTagCodec
 
THOUSAND_GENOMES_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
tid - Variable in class htsjdk.tribble.util.TabixUtils.TIntv
 
TimeChannel - Class in htsjdk.samtools.apps
 
TimeChannel() - Constructor for class htsjdk.samtools.apps.TimeChannel
 
TimeRandomAccessFile - Class in htsjdk.samtools.apps
 
TimeRandomAccessFile() - Constructor for class htsjdk.samtools.apps.TimeRandomAccessFile
 
TIndex() - Constructor for class htsjdk.tribble.readers.TabixReader.TIndex
 
TIndex() - Constructor for class htsjdk.tribble.util.TabixUtils.TIndex
 
TIntv() - Constructor for class htsjdk.tribble.util.TabixUtils.TIntv
 
tMap - Variable in class htsjdk.samtools.cram.structure.CompressionHeader
 
toArray() - Method in class htsjdk.samtools.util.DiskBackedQueue

Not supported at this time

toArray(T1[]) - Method in class htsjdk.samtools.util.DiskBackedQueue

Not supported at this time

toArray() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
toArray(T[]) - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
toBriefString() - Method in class htsjdk.variant.variantcontext.Genotype
 
toBufferedStream(InputStream) - Static method in class htsjdk.samtools.util.IOUtil

Wrap the given stream in a BufferedInputStream, if it isn't already wrapper

toByteArray() - Method in class htsjdk.samtools.cram.encoding.BetaIntegerEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding
 
toByteArray() - Method in interface htsjdk.samtools.cram.encoding.Encoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.ExternalByteArrayEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.ExternalByteEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.ExternalIntegerEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.ExternalLongEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.GammaIntegerEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.GolombIntegerEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.GolombLongEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.GolombRiceIntegerEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanByteEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.NullEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.encoding.SubexponentialIntegerEncoding
 
toByteArray() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
 
toChunkList(long[]) - Static method in class htsjdk.samtools.BAMFileSpan

The list of chunks is often represented as an array of
 longs where every even-numbered index is a start coordinate
 and every odd-numbered index is a stop coordinate.

toCoordinateArray() - Method in class htsjdk.samtools.BAMFileSpan

Convert the chunk list to an array of offsets, paired in [start,end) format.

toDiploidGenotype(String) - Static method in enum htsjdk.tribble.gelitext.DiploidGenotype

Deprecated.
 
toHeaderVersion(String) - Static method in enum htsjdk.variant.vcf.VCFHeaderVersion

get the header version

toHexDigit(int) - Static method in class htsjdk.samtools.util.StringUtil
 
toList() - Method in interface htsjdk.samtools.util.CloseableIterator

Consumes the contents of the iterator and returns it as a List.

toList(Class<T>, Object) - Static method in class htsjdk.variant.bcf2.BCF2Utils

Helper function that takes an object and returns a list representation
 of it:

 o == null => []
 o is a list => o
 else => [o]

toLowerCase(byte) - Static method in class htsjdk.samtools.util.StringUtil
 
toParam(int, int) - Static method in class htsjdk.samtools.cram.encoding.BetaIntegerEncoding
 
toParam(EncodingParams, EncodingParams) - Static method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
 
toParam(byte, int) - Static method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding
 
toParam(int) - Static method in class htsjdk.samtools.cram.encoding.ExternalByteArrayEncoding
 
toParam(int) - Static method in class htsjdk.samtools.cram.encoding.ExternalByteEncoding
 
toParam(int) - Static method in class htsjdk.samtools.cram.encoding.ExternalIntegerEncoding
 
toParam(int) - Static method in class htsjdk.samtools.cram.encoding.ExternalLongEncoding
 
toParam(int) - Static method in class htsjdk.samtools.cram.encoding.GammaIntegerEncoding
 
toParam(int) - Static method in class htsjdk.samtools.cram.encoding.GolombIntegerEncoding
 
toParam(int, int) - Static method in class htsjdk.samtools.cram.encoding.GolombIntegerEncoding
 
toParam(int, int) - Static method in class htsjdk.samtools.cram.encoding.GolombLongEncoding
 
toParam(int, int) - Static method in class htsjdk.samtools.cram.encoding.GolombRiceIntegerEncoding
 
toParam(byte[], int[]) - Static method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanByteEncoding
 
toParam(int[], int[]) - Static method in class htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding
 
toParam() - Static method in class htsjdk.samtools.cram.encoding.NullEncoding
 
toParam(int, int) - Static method in class htsjdk.samtools.cram.encoding.SubexponentialIntegerEncoding
 
toStrand(String) - Static method in enum htsjdk.tribble.annotation.Strand

provide a way to take an encoding string, and produce a Strand

toString() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord

Simple to String that outputs the concrete class name and the set of attributes stored.

toString() - Method in class htsjdk.samtools.BAMFileSpan

Creates a string representation of this chunk list.

toString() - Method in class htsjdk.samtools.Chunk
 
toString() - Method in class htsjdk.samtools.Cigar
 
toString() - Method in class htsjdk.samtools.CigarElement
 
toString() - Method in enum htsjdk.samtools.CigarOperator

Returns the cigar operator as it would be seen in a SAM file.

toString() - Method in class htsjdk.samtools.cram.common.Version
 
toString() - Method in class htsjdk.samtools.cram.CRAIEntry
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
 
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
 
toString() - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
toString() - Method in class htsjdk.samtools.cram.lossy.BaseCategory
 
toString() - Method in class htsjdk.samtools.cram.lossy.PreservationPolicy
 
toString() - Method in class htsjdk.samtools.cram.lossy.QualityScoreTreatment
 
toString() - Method in class htsjdk.samtools.cram.lossy.ReadCategory
 
toString() - Method in class htsjdk.samtools.cram.structure.Block
 
toString() - Method in class htsjdk.samtools.cram.structure.Container
 
toString() - Method in class htsjdk.samtools.cram.structure.CramCompressionRecord
 
toString() - Method in class htsjdk.samtools.cram.structure.EncodingParams
 
toString() - Method in class htsjdk.samtools.cram.structure.Slice
 
toString() - Method in class htsjdk.samtools.cram.structure.SubstitutionMatrix
 
toString() - Method in class htsjdk.samtools.fastq.FastqReader
 
toString() - Method in class htsjdk.samtools.fastq.FastqRecord
 
toString() - Method in class htsjdk.samtools.liftover.LiftOver.PartialLiftover
 
toString() - Method in interface htsjdk.samtools.metrics.Header

Converts the header to a String for persisting to a file.

toString() - Method in class htsjdk.samtools.metrics.MetricBase

Converts the metric class to a human readable string.

toString() - Method in class htsjdk.samtools.metrics.StringHeader
 
toString() - Method in class htsjdk.samtools.metrics.VersionHeader
 
toString() - Method in class htsjdk.samtools.QueryInterval
 
toString() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile

A simple toString implementation for debugging.

toString() - Method in class htsjdk.samtools.reference.ReferenceSequence
 
toString() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
 
toString() - Method in class htsjdk.samtools.SAMFileWriterFactory
 
toString() - Method in class htsjdk.samtools.SamInputResource
 
toString() - Method in class htsjdk.samtools.SAMRecord

Simple toString() that gives a little bit of useful info about the read.

toString() - Method in class htsjdk.samtools.SAMSequenceDictionary
 
toString() - Method in class htsjdk.samtools.SAMSequenceRecord
 
toString() - Method in class htsjdk.samtools.SAMValidationError
 
toString() - Method in class htsjdk.samtools.sra.SRAAccession
 
toString() - Method in class htsjdk.samtools.util.AbstractLocusInfo
 
toString() - Method in class htsjdk.samtools.util.Histogram.Bin

Returns the String format for the value in the bin.

toString() - Method in class htsjdk.samtools.util.Histogram
 
toString() - Method in class htsjdk.samtools.util.Interval
 
toString() - Method in class htsjdk.samtools.util.IntervalTree.Node
 
toString() - Method in class htsjdk.samtools.util.Iso8601Date
 
toString() - Method in class htsjdk.samtools.util.RelativeIso8601Date

Returns a String representation of this date.

toString() - Method in class htsjdk.samtools.util.Tuple
 
toString() - Method in class htsjdk.tribble.index.interval.Interval
 
toString() - Method in class htsjdk.tribble.index.interval.IntervalTree
 
toString() - Method in class htsjdk.tribble.readers.TabixReader
 
toString() - Method in class htsjdk.variant.bcf2.BCF2Codec.SitesInfoForDecoding
 
toString() - Method in class htsjdk.variant.bcf2.BCFVersion
 
toString() - Method in class htsjdk.variant.variantcontext.Allele
 
toString() - Method in class htsjdk.variant.variantcontext.Genotype
 
toString() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
 
toString() - Method in class htsjdk.variant.variantcontext.GenotypesContext
 
toString() - Method in class htsjdk.variant.variantcontext.VariantContext
 
toString() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
 
toString() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
 
toString() - Method in class htsjdk.variant.vcf.VCFHeader
 
toString() - Method in class htsjdk.variant.vcf.VCFHeaderLine
 
toStringDecodeGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContext
 
toStringEncoding() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine

make a string representation of this header line

toStringEncoding() - Method in class htsjdk.variant.vcf.VCFHeaderLine

Should be overloaded in sub classes to do subclass specific

toStringEncoding(Map<String, ? extends Object>) - Static method in class htsjdk.variant.vcf.VCFHeaderLine

create a string of a mapping pair for the target VCF version

toStringEncoding() - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
 
toStringIfExists(String, int) - Static method in class htsjdk.variant.variantcontext.Genotype

Returns a display name for field name with value v if this isn't -1.

toStringIfExists(String, String) - Static method in class htsjdk.variant.variantcontext.Genotype

Returns a display name for field name with String value v if this isn't null.

toStringIfExists(String, int[]) - Static method in class htsjdk.variant.variantcontext.Genotype

Returns a display name for field name with values vs if this isn't null.

toStringWithoutGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContext
 
toTwoBytes(EncodingKey) - Static method in enum htsjdk.samtools.cram.structure.EncodingKey
 
toUpperCase(byte) - Static method in class htsjdk.samtools.util.StringUtil
 
toUpperCase(byte[]) - Static method in class htsjdk.samtools.util.StringUtil

Converts in place all lower case letters to upper case in the byte array provided.

TPair64(long, long) - Constructor for class htsjdk.tribble.readers.TabixReader.TPair64
 
TPair64(TabixReader.TPair64) - Constructor for class htsjdk.tribble.readers.TabixReader.TPair64
 
TPair64(long, long) - Constructor for class htsjdk.tribble.util.TabixUtils.TPair64
 
TPair64(TabixUtils.TPair64) - Constructor for class htsjdk.tribble.util.TabixUtils.TPair64
 
transferByStream(InputStream, OutputStream, long) - Static method in class htsjdk.samtools.util.IOUtil

Transfers from the input stream to the output stream using stream operations and a buffer.

treatment - Variable in class htsjdk.samtools.cram.lossy.PreservationPolicy
 
Tribble - Class in htsjdk.tribble

Common, tribble wide constants and static functions

TribbleException - Exception in htsjdk.tribble
 
TribbleException(String) - Constructor for exception htsjdk.tribble.TribbleException
 
TribbleException(String, Throwable) - Constructor for exception htsjdk.tribble.TribbleException
 
TribbleException.FeatureFileDoesntExist - Exception in htsjdk.tribble
 
TribbleException.InternalCodecException - Exception in htsjdk.tribble
 
TribbleException.InvalidDecodeLine - Exception in htsjdk.tribble
 
TribbleException.InvalidHeader - Exception in htsjdk.tribble
 
TribbleException.MalformedFeatureFile - Exception in htsjdk.tribble
 
TribbleException.TabixReaderFailure - Exception in htsjdk.tribble
 
TribbleException.UnableToCreateCorrectIndexType - Exception in htsjdk.tribble
 
TribbleException.UnableToReadIndexFile - Exception in htsjdk.tribble
 
TribbleIndexCreator - Class in htsjdk.tribble.index

Base class for Tribble-specific index creators.

TribbleIndexCreator() - Constructor for class htsjdk.tribble.index.TribbleIndexCreator
 
TribbleIndexedFeatureReader<T extends Feature,SOURCE> - Class in htsjdk.tribble

A reader for text feature files  (i.e.

TribbleIndexedFeatureReader(String, FeatureCodec<T, SOURCE>, boolean) - Constructor for class htsjdk.tribble.TribbleIndexedFeatureReader
 
TribbleIndexedFeatureReader(String, String, FeatureCodec<T, SOURCE>, boolean) - Constructor for class htsjdk.tribble.TribbleIndexedFeatureReader
 
TribbleIndexedFeatureReader(String, FeatureCodec<T, SOURCE>, Index) - Constructor for class htsjdk.tribble.TribbleIndexedFeatureReader
 
trim(String, char) - Static method in class htsjdk.tribble.util.ParsingUtils
 
trimByTailLimit(int) - Method in class htsjdk.samtools.util.Histogram

Trims the histogram when the bins in the tail of the distribution contain fewer than mode/tailLimit items

trimByWidth(int) - Method in class htsjdk.samtools.util.Histogram

Trims the histogram so that only bins <= width are kept.

TrimmingUtil - Class in htsjdk.samtools.util

Utility code for performing quality trimming.

TrimmingUtil() - Constructor for class htsjdk.samtools.util.TrimmingUtil
 
truncateSequenceName(String) - Static method in class htsjdk.samtools.SAMSequenceRecord

Truncate sequence name at first whitespace.

Tuple<A,B> - Class in htsjdk.samtools.util

A simple tuple class.

Tuple(A, B) - Constructor for class htsjdk.samtools.util.Tuple
 
TWO_GBS - Static variable in class htsjdk.samtools.util.IOUtil
 
type - Variable in class htsjdk.samtools.cram.lossy.BaseCategory
 
type - Variable in class htsjdk.samtools.cram.lossy.QualityScoreTreatment
 
type - Variable in class htsjdk.samtools.cram.lossy.ReadCategory
 
type() - Method in class htsjdk.samtools.CRAMFileReader
 
type() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
 
type() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
 
type() - Method in interface htsjdk.samtools.SamReader
 
Type() - Constructor for class htsjdk.samtools.SamReader.Type
 
type() - Method in class htsjdk.samtools.SRAFileReader
 
type - Variable in class htsjdk.variant.variantcontext.VariantContext

The type (cached for performance reasons) of this context





U

u - Variable in class htsjdk.tribble.util.TabixUtils.TPair64
 
U2 - Variable in class htsjdk.samtools.SAMTagUtil
 
UCSC_FLAGS - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
 
UnableToCreateCorrectIndexType(String, Exception) - Constructor for exception htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType
 
UnableToCreateCorrectIndexType(String) - Constructor for exception htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType
 
UnableToReadIndexFile(String, String, Exception) - Constructor for exception htsjdk.tribble.TribbleException.UnableToReadIndexFile
 
UNBOUND_DESCRIPTION - Static variable in class htsjdk.variant.vcf.VCFHeaderLine
 
UNBOUNDED_ENCODING_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
UNBOUNDED_ENCODING_v4 - Static variable in class htsjdk.variant.vcf.VCFConstants
 
unbzip2(byte[]) - Static method in class htsjdk.samtools.cram.io.ExternalCompression

Uncompress a BZIP2 data blob into a new byte array.

uncompress(ByteBuffer, ByteBuffer) - Static method in class htsjdk.samtools.cram.encoding.rans.RANS
 
UNEXPECTED_BLOCK_LENGTH_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
 
unfiltered() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder

This genotype is unfiltered

unfiltered() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder

Tells this builder that the resulting VariantContext be unfiltered

UNFILTERED - Static variable in class htsjdk.variant.vcf.VCFConstants
 
union(Collection<IntervalList>) - Static method in class htsjdk.samtools.util.IntervalList

A utility function for finding the union of a list of IntervalLists, checks for equal dictionaries.

union(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
 
unique() - Method in class htsjdk.samtools.util.IntervalList

Deprecated.
use IntervalList.uniqued() instead.


unique(boolean) - Method in class htsjdk.samtools.util.IntervalList

Deprecated.
use IntervalList.uniqued(boolean) instead.


uniqued() - Method in class htsjdk.samtools.util.IntervalList

Returned an independent IntervalList that is sorted and uniquified.

uniqued(boolean) - Method in class htsjdk.samtools.util.IntervalList

Returned an independent IntervalList that is sorted and uniquified.

UNKNOWN_MAPPING_QUALITY - Static variable in class htsjdk.samtools.SAMRecord

Alignment score for a good alignment, but where computing a Phred-score is not feasible.

UNKNOWN_READ_GROUP_ID - Static variable in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
UNKNOWN_READ_GROUP_SAMPLE - Static variable in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
UNKNOWN_SEQUENCE_LENGTH - Static variable in class htsjdk.samtools.SAMSequenceRecord

If one sequence has this length, and another sequence had a different length, isSameSequence will
 not complain that they are different sequences.

UNMAPPED_SPAN - Static variable in class htsjdk.samtools.cram.structure.AlignmentSpan

A constant to represent an unmapped span.

UNPHASED - Static variable in class htsjdk.variant.vcf.VCFConstants
 
UNPHASED_ALLELE_SEPARATOR - Static variable in class htsjdk.variant.variantcontext.Genotype
 
unplaced() - Static method in class htsjdk.samtools.cram.lossy.ReadCategory
 
unrans(byte[]) - Static method in class htsjdk.samtools.cram.io.ExternalCompression

Uncompress a rANS data blob into a new byte array.

unrollFiles(Collection<File>, String...) - Static method in class htsjdk.samtools.util.IOUtil

Go through the files provided and if they have one of the provided file extensions pass the file into the output
 otherwise assume that file is a list of filenames and unfold it into the output.

UNSET_GENOMIC_LOCATION - Static variable in class htsjdk.samtools.GenomicIndexUtil

E.g.

unsetBuffering() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Do not use buffering in the next VariantContextWriter created by this builder.

unsetCreateMD5() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Don't create an MD5 digest file for the next VariantContextWriter created by this builder.

unsetDefaultOption(Options) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Remove an option from the set of default Options that will be used as the initial set of options
 for all VariantContextWriterBuilders created after this call.

unsetOption(Options) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Remove one option from the set of Options for the VariantContextWriterBuilder, if it's present.

unsetQualityScore - Static variable in class htsjdk.samtools.cram.build.Sam2CramRecordFactory
 
UnsortedFileException - Exception in htsjdk.tribble.exception

an exception for when we've discovered that an input file is unsorted; sorted files are required by Tribble

UnsortedFileException(Throwable) - Constructor for exception htsjdk.tribble.exception.UnsortedFileException
 
UnsortedFileException(String, Throwable) - Constructor for exception htsjdk.tribble.exception.UnsortedFileException
 
UnsortedFileException(String) - Constructor for exception htsjdk.tribble.exception.UnsortedFileException
 
UnsortedFileException() - Constructor for exception htsjdk.tribble.exception.UnsortedFileException
 
unxz(byte[]) - Static method in class htsjdk.samtools.cram.io.ExternalCompression

Uncompress a XZ data blob into a new byte array.

unzipBlock(byte[], byte[], int) - Method in class htsjdk.samtools.util.BlockGunzipper

Decompress GZIP-compressed data

unzipBlock(byte[], int, byte[], int, int) - Method in class htsjdk.samtools.util.BlockGunzipper

Decompress GZIP-compressed data

updateLongestFeature(int) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
upperCase(byte) - Static method in class htsjdk.samtools.util.SequenceUtil
 
upperCase(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
 
UQ - Variable in class htsjdk.samtools.SAMTagUtil
 
URI_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
 
URLHelper - Interface in htsjdk.tribble.util

Interface defining a helper class for dealing with URL resources.

urlHelperClass - Static variable in class htsjdk.tribble.util.ParsingUtils
 
USE_ASYNC_IO_READ_FOR_SAMTOOLS - Static variable in class htsjdk.samtools.Defaults

Should asynchronous read I/O be used where supported by the samtools package (one thread per file).

USE_ASYNC_IO_WRITE_FOR_SAMTOOLS - Static variable in class htsjdk.samtools.Defaults

Should asynchronous write I/O be used where supported by the samtools package (one thread per file).

USE_ASYNC_IO_WRITE_FOR_TRIBBLE - Static variable in class htsjdk.samtools.Defaults

Should asynchronous write I/O be used where supported by the tribble package (one thread per file).

USE_CRAM_REF_DOWNLOAD - Static variable in class htsjdk.samtools.Defaults

Boolean describing whether downloading a reference file is allowed (for CRAM files),
 in case the reference file is not specified by the user
 Enabling this is not necessarily a good idea, since this process often fails

UserPasswordInput - Interface in htsjdk.samtools.seekablestream
 
Utils - Class in htsjdk.samtools.cram.build
 




V

v - Variable in class htsjdk.tribble.util.TabixUtils.TPair64
 
VALID_BASES_LOWER - Static variable in class htsjdk.samtools.util.SequenceUtil
 
VALID_BASES_UPPER - Static variable in class htsjdk.samtools.util.SequenceUtil
 
validate - Static variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
validateAlternateAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext
 
validateBamFileTermination(File) - Method in class htsjdk.samtools.SamFileValidator
 
validateChromosomeCounts() - Method in class htsjdk.variant.variantcontext.VariantContext
 
validateCigar(long) - Method in class htsjdk.samtools.SAMRecord

Run all validations of CIGAR.

validateCigar(SAMRecord, Cigar, Integer, List<AlignmentBlock>, long, String) - Static method in class htsjdk.samtools.SAMUtils

Run all validations of the mate's CIGAR.

VALIDATED_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
 
validateIndexHeader(int, LittleEndianInputStream) - Method in class htsjdk.tribble.index.AbstractIndex
 
validateMateCigar(SAMRecord, long) - Static method in class htsjdk.samtools.SAMUtils

Run all validations of the mate's CIGAR.

validateOffset(int, byte[]) - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
 
validateReferenceBases(Allele, Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
 
validateRefMD5(byte[]) - Method in class htsjdk.samtools.cram.structure.Slice
 
validateRSIDs(Set<String>) - Method in class htsjdk.variant.variantcontext.VariantContext
 
validateSamFileSummary(SamReader, ReferenceSequenceFile) - Method in class htsjdk.samtools.SamFileValidator

Outputs validation summary report to out.

validateSamFileVerbose(SamReader, ReferenceSequenceFile) - Method in class htsjdk.samtools.SamFileValidator

Outputs validation error details to out.

validateSequenceName(String) - Static method in class htsjdk.samtools.SAMSequenceRecord

Throw an exception if the sequence name is not valid.

validateToSequences(SAMSequenceDictionary) - Method in class htsjdk.samtools.liftover.LiftOver

Throw an exception if all the "to" sequence names in the chains are not found in the given sequence dictionary.

ValidationMetrics() - Constructor for class htsjdk.samtools.SamFileValidator.ValidationMetrics
 
validationStringency() - Method in class htsjdk.samtools.SamReaderFactory
 
validationStringency(ValidationStringency) - Method in class htsjdk.samtools.SamReaderFactory

Set this factory's ValidationStringency to the provided one, then returns itself.

ValidationStringency - Enum in htsjdk.samtools

How strict to be when reading a SAM or BAM, beyond bare minimum validation.

value - Variable in class htsjdk.samtools.cram.common.MutableInt
 
value - Variable in class htsjdk.samtools.SAMBinaryTagAndValue
 
value - Variable in class htsjdk.samtools.SAMRecord.SAMTagAndValue
 
value - Variable in class htsjdk.samtools.TagValueAndUnsignedArrayFlag
 
value() - Method in enum htsjdk.tribble.bed.BEDCodec.StartOffset
 
valueOf(String) - Static method in enum htsjdk.samtools.BamIndexValidator.IndexValidationStringency

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.CigarOperator

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.encoding.DataSeriesType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.encoding.rans.RANS.ORDER

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.lossy.BaseCategoryType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.lossy.QualityScoreTreatmentType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.lossy.ReadCategoryType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.structure.BlockCompressionMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.structure.BlockContentType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.structure.EncodingID

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.cram.structure.EncodingKey

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.DownsamplingIteratorFactory.Strategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.fastq.FastqConstants.FastqExtensions

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SAMFileHeader.GroupOrder

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SAMFileHeader.SortOrder

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SAMFlag

Returns the enum constant of this type with the specified name.

valueOf(int) - Static method in enum htsjdk.samtools.SAMFlag
 
valueOf(String) - Static method in enum htsjdk.samtools.SamFlagField

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SamIndexes

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SamPairUtil.PairOrientation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SamReaderFactory.Option

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SAMReadGroupRecord.PlatformValue

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SAMTag

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SAMValidationError.Severity

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SAMValidationError.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.SQTagUtil.SQBase

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.util.BlockCompressedInputStream.FileTermination

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.util.EdgingRecordAndOffset.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.util.FastqQualityFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.util.Log.LogLevel

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.util.QualityEncodingDetector.FileContext

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.samtools.ValidationStringency

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.tribble.annotation.Strand

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.tribble.bed.BEDCodec.StartOffset

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.tribble.gelitext.DiploidGenotype

Deprecated.
Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.tribble.index.AbstractIndex.IndexType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.tribble.index.IndexFactory.IndexBalanceApproach

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.tribble.index.IndexFactory.IndexType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.tribble.readers.LineReaderUtil.LineReaderOption

Deprecated.
Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.bcf2.BCF2Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.variantcontext.GenotypeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.variantcontext.JexlMissingValueTreatment

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.variantcontext.StructuralVariantType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.variantcontext.VariantContext.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.variantcontext.VariantContext.Validation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.variantcontext.writer.Options

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.vcf.VCFHeaderLineCount

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.vcf.VCFHeaderLineType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum htsjdk.variant.vcf.VCFHeaderVersion

Returns the enum constant of this type with the specified name.

values() - Static method in enum htsjdk.samtools.BamIndexValidator.IndexValidationStringency

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.CigarOperator

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.encoding.DataSeriesType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.encoding.rans.RANS.ORDER

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.lossy.BaseCategoryType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.lossy.QualityScoreTreatmentType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.lossy.ReadCategoryType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.structure.BlockCompressionMethod

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.structure.BlockContentType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.structure.EncodingID

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.cram.structure.EncodingKey

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.DownsamplingIteratorFactory.Strategy

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.fastq.FastqConstants.FastqExtensions

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SAMFileHeader.GroupOrder

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SAMFileHeader.SortOrder

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SAMFlag

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SamFlagField

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SamIndexes

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SamPairUtil.PairOrientation

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SamReaderFactory.Option

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SAMReadGroupRecord.PlatformValue

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SAMTag

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SAMValidationError.Severity

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SAMValidationError.Type

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.SQTagUtil.SQBase

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.util.BlockCompressedInputStream.FileTermination

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.util.EdgingRecordAndOffset.Type

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.util.FastqQualityFormat

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Method in class htsjdk.samtools.util.Histogram

Returns a Collection view of the values contained in this histogram.

values() - Static method in enum htsjdk.samtools.util.Log.LogLevel

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.util.QualityEncodingDetector.FileContext

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.samtools.ValidationStringency

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.tribble.annotation.Strand

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.tribble.bed.BEDCodec.StartOffset

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.tribble.gelitext.DiploidGenotype

Deprecated.
Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.tribble.index.AbstractIndex.IndexType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.tribble.index.IndexFactory.IndexBalanceApproach

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.tribble.index.IndexFactory.IndexType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.tribble.readers.LineReaderUtil.LineReaderOption

Deprecated.
Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.bcf2.BCF2Type

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.variantcontext.GenotypeType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.variantcontext.JexlMissingValueTreatment

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.variantcontext.StructuralVariantType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.variantcontext.VariantContext.Type

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.variantcontext.VariantContext.Validation

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.variantcontext.writer.Options

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.vcf.VCFHeaderLineCount

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.vcf.VCFHeaderLineType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum htsjdk.variant.vcf.VCFHeaderVersion

Returns an array containing the constants of this enum type, in
the order they are declared.

ValuesIterator(Iterator<IntervalTree.Node<V1>>) - Constructor for class htsjdk.samtools.util.IntervalTree.ValuesIterator
 
variance() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
 
VariantContext - Class in htsjdk.variant.variantcontext

 High-level overview

VariantContext(VariantContext) - Constructor for class htsjdk.variant.variantcontext.VariantContext

Copy constructor

VariantContext(String, String, String, long, long, Collection<Allele>, GenotypesContext, double, Set<String>, Map<String, Object>, boolean, EnumSet<VariantContext.Validation>) - Constructor for class htsjdk.variant.variantcontext.VariantContext

the actual constructor.

VariantContext.Type - Enum in htsjdk.variant.variantcontext
 
VariantContext.Validation - Enum in htsjdk.variant.variantcontext
 
VariantContextBuilder - Class in htsjdk.variant.variantcontext

Builder class for VariantContext.

VariantContextBuilder() - Constructor for class htsjdk.variant.variantcontext.VariantContextBuilder

Create an empty VariantContextBuilder where all values adopt their default values.

VariantContextBuilder(String, String, long, long, Collection<Allele>) - Constructor for class htsjdk.variant.variantcontext.VariantContextBuilder

Create an empty VariantContextBuilder where all values adopt their default values, but the bare min.

VariantContextBuilder(VariantContext) - Constructor for class htsjdk.variant.variantcontext.VariantContextBuilder

Returns a new builder based on parent -- the new VC will have all fields initialized
 to their corresponding values in parent.

VariantContextBuilder(VariantContextBuilder) - Constructor for class htsjdk.variant.variantcontext.VariantContextBuilder
 
VariantContextComparator - Class in htsjdk.variant.variantcontext

A Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List
 provided at construction time, then by start position with each contig/chromosome.

VariantContextComparator(List<String>) - Constructor for class htsjdk.variant.variantcontext.VariantContextComparator
 
VariantContextComparator(Collection<VCFContigHeaderLine>) - Constructor for class htsjdk.variant.variantcontext.VariantContextComparator

Creates a VariantContextComparator from the given VCF contig header lines.

VariantContextComparator(SAMSequenceDictionary) - Constructor for class htsjdk.variant.variantcontext.VariantContextComparator
 
VariantContextFilter - Interface in htsjdk.variant.variantcontext.filter

API for filtering VariantContexts

VariantContextUtils - Class in htsjdk.variant.variantcontext
 
VariantContextUtils() - Constructor for class htsjdk.variant.variantcontext.VariantContextUtils
 
VariantContextUtils.JexlVCMatchExp - Class in htsjdk.variant.variantcontext

A simple but common wrapper for matching VariantContext objects using JEXL expressions

VariantContextWriter - Interface in htsjdk.variant.variantcontext.writer

this class writes VCF files

VariantContextWriterBuilder - Class in htsjdk.variant.variantcontext.writer
 
VariantContextWriterBuilder() - Constructor for class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

Default constructor.

VariantContextWriterBuilder.OutputType - Enum in htsjdk.variant.variantcontext.writer
 
VariantContextWriterFactory - Class in htsjdk.variant.variantcontext.writer

Deprecated.
Replaced by VariantContextWriterBuilder


VCF - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
 
VCF3_MAGIC_HEADER - Static variable in class htsjdk.variant.vcf.VCF3Codec
 
VCF3Codec - Class in htsjdk.variant.vcf

A feature codec for the VCF3 specification, to read older VCF files.

VCF3Codec() - Constructor for class htsjdk.variant.vcf.VCF3Codec
 
VCF4_MAGIC_HEADER - Static variable in class htsjdk.variant.vcf.VCFCodec
 
VCF_CHARSET - Static variable in class htsjdk.variant.vcf.VCFEncoder

The encoding used for VCF files: ISO-8859-1

VCF_ENCODING_EPSILON - Static variable in class htsjdk.variant.vcf.VCFConstants
 
VCF_EXTENSIONS - Static variable in class htsjdk.samtools.util.IOUtil

Possible extensions for VCF files and related formats.

VCF_FLAGS - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
 
VCF_LOCALE - Static variable in class htsjdk.variant.vcf.VCFConstants
 
VCFCodec - Class in htsjdk.variant.vcf

A feature codec for the VCF 4 specification

VCFCodec() - Constructor for class htsjdk.variant.vcf.VCFCodec
 
VCFCompoundHeaderLine - Class in htsjdk.variant.vcf

a base class for compound header lines, which include info lines and format lines (so far)

VCFCompoundHeaderLine(String, int, VCFHeaderLineType, String, VCFCompoundHeaderLine.SupportedHeaderLineType) - Constructor for class htsjdk.variant.vcf.VCFCompoundHeaderLine

create a VCF format header line

VCFCompoundHeaderLine(String, VCFHeaderLineCount, VCFHeaderLineType, String, VCFCompoundHeaderLine.SupportedHeaderLineType) - Constructor for class htsjdk.variant.vcf.VCFCompoundHeaderLine

create a VCF format header line

VCFCompoundHeaderLine(String, VCFHeaderVersion, VCFCompoundHeaderLine.SupportedHeaderLineType) - Constructor for class htsjdk.variant.vcf.VCFCompoundHeaderLine

create a VCF format header line

VCFCompoundHeaderLine.SupportedHeaderLineType - Enum in htsjdk.variant.vcf
 
VCFConstants - Class in htsjdk.variant.vcf
 
VCFConstants() - Constructor for class htsjdk.variant.vcf.VCFConstants
 
VCFContigHeaderLine - Class in htsjdk.variant.vcf

A special class representing a contig VCF header line.

VCFContigHeaderLine(String, VCFHeaderVersion, String, int) - Constructor for class htsjdk.variant.vcf.VCFContigHeaderLine

create a VCF contig header line

VCFContigHeaderLine(Map<String, String>, int) - Constructor for class htsjdk.variant.vcf.VCFContigHeaderLine
 
VCFEncoder - Class in htsjdk.variant.vcf

Functions specific to encoding VCF records.

VCFEncoder(VCFHeader, boolean, boolean) - Constructor for class htsjdk.variant.vcf.VCFEncoder

Prepare a VCFEncoder that will encode records appropriate to the given VCF header, optionally
 allowing missing fields in the header.

VCFFileReader - Class in htsjdk.variant.vcf

Simplified interface for reading from VCF/BCF files.

VCFFileReader(File) - Constructor for class htsjdk.variant.vcf.VCFFileReader

Constructs a VCFFileReader that requires the index to be present.

VCFFileReader(File, File) - Constructor for class htsjdk.variant.vcf.VCFFileReader

Constructs a VCFFileReader with a specified index.

VCFFileReader(File, boolean) - Constructor for class htsjdk.variant.vcf.VCFFileReader

Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.

VCFFileReader(File, File, boolean) - Constructor for class htsjdk.variant.vcf.VCFFileReader

Allows construction of a VCFFileReader with a specified index file.

VCFFilterHeaderLine - Class in htsjdk.variant.vcf
 
VCFFilterHeaderLine(String, String) - Constructor for class htsjdk.variant.vcf.VCFFilterHeaderLine

create a VCF filter header line

VCFFilterHeaderLine(String) - Constructor for class htsjdk.variant.vcf.VCFFilterHeaderLine

Convenience constructor for FILTER whose description is the name

VCFFilterHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFFilterHeaderLine

create a VCF info header line

VCFFormatHeaderLine - Class in htsjdk.variant.vcf
 
VCFFormatHeaderLine(String, int, VCFHeaderLineType, String) - Constructor for class htsjdk.variant.vcf.VCFFormatHeaderLine
 
VCFFormatHeaderLine(String, VCFHeaderLineCount, VCFHeaderLineType, String) - Constructor for class htsjdk.variant.vcf.VCFFormatHeaderLine
 
VCFFormatHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFFormatHeaderLine
 
VCFHeader - Class in htsjdk.variant.vcf

A class to represent a VCF header

VCFHeader() - Constructor for class htsjdk.variant.vcf.VCFHeader

Create an empty VCF header with no header lines and no samples

VCFHeader(Set<VCFHeaderLine>) - Constructor for class htsjdk.variant.vcf.VCFHeader

create a VCF header, given a list of meta data and auxiliary tags

VCFHeader(VCFHeader) - Constructor for class htsjdk.variant.vcf.VCFHeader

Creates a deep copy of the given VCFHeader, duplicating all its metadata and
 sample names.

VCFHeader(Set<VCFHeaderLine>, Set<String>) - Constructor for class htsjdk.variant.vcf.VCFHeader

create a VCF header, given a list of meta data and auxillary tags

VCFHeader(Set<VCFHeaderLine>, List<String>) - Constructor for class htsjdk.variant.vcf.VCFHeader
 
VCFHeader.HEADER_FIELDS - Enum in htsjdk.variant.vcf
 
VCFHeaderLine - Class in htsjdk.variant.vcf
 
VCFHeaderLine(String, String) - Constructor for class htsjdk.variant.vcf.VCFHeaderLine

create a VCF header line

VCFHeaderLineCount - Enum in htsjdk.variant.vcf

the count encodings we use for fields in VCF header lines

VCFHeaderLineTranslator - Class in htsjdk.variant.vcf

A class for translating between vcf header versions

VCFHeaderLineTranslator() - Constructor for class htsjdk.variant.vcf.VCFHeaderLineTranslator
 
VCFHeaderLineType - Enum in htsjdk.variant.vcf

the type encodings we use for fields in VCF header lines

VCFHeaderVersion - Enum in htsjdk.variant.vcf

information that identifies each header version

VCFIDHeaderLine - Interface in htsjdk.variant.vcf

an interface for ID-based header lines

VCFInfoHeaderLine - Class in htsjdk.variant.vcf
 
VCFInfoHeaderLine(String, int, VCFHeaderLineType, String) - Constructor for class htsjdk.variant.vcf.VCFInfoHeaderLine
 
VCFInfoHeaderLine(String, VCFHeaderLineCount, VCFHeaderLineType, String) - Constructor for class htsjdk.variant.vcf.VCFInfoHeaderLine
 
VCFInfoHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFInfoHeaderLine
 
VCFRecordCodec - Class in htsjdk.variant.vcf

Writes VariantContext instances to an OutputStream without headers or metadata.

VCFRecordCodec(VCFHeader) - Constructor for class htsjdk.variant.vcf.VCFRecordCodec
 
VCFRecordCodec(VCFHeader, boolean) - Constructor for class htsjdk.variant.vcf.VCFRecordCodec
 
VCFSimpleHeaderLine - Class in htsjdk.variant.vcf
 
VCFSimpleHeaderLine(String, String, String) - Constructor for class htsjdk.variant.vcf.VCFSimpleHeaderLine

create a VCF filter header line

VCFSimpleHeaderLine(String, VCFHeaderVersion, String, List<String>) - Constructor for class htsjdk.variant.vcf.VCFSimpleHeaderLine

create a VCF info header line

VCFSimpleHeaderLine(String, Map<String, String>) - Constructor for class htsjdk.variant.vcf.VCFSimpleHeaderLine
 
VCFStandardHeaderLines - Class in htsjdk.variant.vcf

Manages header lines for standard VCF

VCFStandardHeaderLines() - Constructor for class htsjdk.variant.vcf.VCFStandardHeaderLines
 
VCFUtils - Class in htsjdk.variant.vcf
 
VCFUtils() - Constructor for class htsjdk.variant.vcf.VCFUtils
 
Version - Class in htsjdk.samtools.cram.common

A class to represent a version information, 3 number: major, minor and build number.

Version(int, int, int) - Constructor for class htsjdk.samtools.cram.common.Version
 
Version(String) - Constructor for class htsjdk.samtools.cram.common.Version
 
VERSION - Static variable in class htsjdk.tribble.index.AbstractIndex
 
version - Variable in class htsjdk.tribble.index.AbstractIndex
 
version - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
VERSION_TAG - Static variable in class htsjdk.samtools.SAMFileHeader
 
VersionHeader - Class in htsjdk.samtools.metrics

Header that stores information about the version of some piece of software or
 data used to create the metrics file.

VersionHeader() - Constructor for class htsjdk.samtools.metrics.VersionHeader
 




W

warn(Throwable, Object...) - Method in class htsjdk.samtools.util.Log

Logs a Throwable and optional message parts at level warn.

warn(Object...) - Method in class htsjdk.samtools.util.Log

Logs one or more message parts at level warn.

warnedAboutNoEqualsForNonFlag - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
 
WholeGenomeReferenceSequenceMask - Class in htsjdk.samtools.util

Implementation of ReferenceSequenceMask that indicates that all the loci in the sequence dictionary are of interest.

WholeGenomeReferenceSequenceMask(SAMFileHeader) - Constructor for class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
 
WholeReadClippedFilter - Class in htsjdk.samtools.filter

Filter SAMRecords so that only those that have at least one un-clipped base are
 returned.

WholeReadClippedFilter() - Constructor for class htsjdk.samtools.filter.WholeReadClippedFilter
 
withinRange(long) - Method in enum htsjdk.variant.bcf2.BCF2Type

Can we encode value v in this type, according to its declared range.

withSamFlagField(SamFlagField) - Method in class htsjdk.samtools.SAMLineParser

Sets the expected SAM flag type expected for all records.

withUpdatedContigs(VCFHeader, File, SAMSequenceDictionary) - Static method in class htsjdk.variant.vcf.VCFUtils

Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary

withUpdatedContigsAsLines(Set<VCFHeaderLine>, File, SAMSequenceDictionary) - Static method in class htsjdk.variant.vcf.VCFUtils
 
withUpdatedContigsAsLines(Set<VCFHeaderLine>, File, SAMSequenceDictionary, boolean) - Static method in class htsjdk.variant.vcf.VCFUtils
 
wordWrap(String, int) - Static method in class htsjdk.samtools.util.StringUtil

Return input string with newlines inserted to ensure that all lines
 have length <= maxLineLength.

wordWrapSingleLine(String, int) - Static method in class htsjdk.samtools.util.StringUtil
 
wouldBeNoCallAllele(byte[]) - Static method in class htsjdk.variant.variantcontext.Allele
 
wouldBeNullAllele(byte[]) - Static method in class htsjdk.variant.variantcontext.Allele
 
wouldBeStarAllele(byte[]) - Static method in class htsjdk.variant.variantcontext.Allele
 
wouldBeSymbolicAllele(byte[]) - Static method in class htsjdk.variant.variantcontext.Allele
 
wrapInputStream(InputStream) - Method in class htsjdk.samtools.util.SnappyLoader

Wrap an InputStream in a SnappyInputStream.

wrapOutputStream(OutputStream) - Method in class htsjdk.samtools.util.SnappyLoader

Wrap an InputStream in a SnappyInputStream.

wrapTempInputStream(InputStream, int) - Method in class htsjdk.samtools.util.TempStreamFactory

Wrap the given InputStream in a SnappyInputStream if available.

wrapTempOutputStream(OutputStream, int) - Method in class htsjdk.samtools.util.TempStreamFactory

Wrap the given OutputStream in a SnappyOutputStream if available.

write(BitOutputStream, T) - Method in class htsjdk.samtools.cram.encoding.AbstractBitCodec
 
write(BitOutputStream, T) - Method in interface htsjdk.samtools.cram.encoding.BitCodec

Write an object into the bit stream

write(BitOutputStream, byte[]) - Method in class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding.ByteArrayStopCodec
 
write(CramCompressionRecord) - Method in class htsjdk.samtools.cram.encoding.writer.Writer
 
write(int, int) - Method in interface htsjdk.samtools.cram.io.BitOutputStream

Write specified number of bits supplied in the integer value.

write(long, int) - Method in interface htsjdk.samtools.cram.io.BitOutputStream

Write specified number of bits supplied in the long value.

write(byte, int) - Method in interface htsjdk.samtools.cram.io.BitOutputStream

Write specified number of bits supplied in the byte value.

write(boolean) - Method in interface htsjdk.samtools.cram.io.BitOutputStream

Write a single bit specified in the boolean argument.

write(boolean, long) - Method in interface htsjdk.samtools.cram.io.BitOutputStream

Write a single bit specified in the boolean argument repeatedly.

write(int[], OutputStream) - Static method in class htsjdk.samtools.cram.io.CramArray

Write CRAM int array to a OutputStream.

write(byte[], int, int) - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
 
write(int) - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
 
write(byte[]) - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
 
write(byte) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(long, int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(int, int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(byte, int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(boolean) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(boolean, long) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(byte[]) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(byte[], int, int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
 
write(int, OutputStream) - Method in class htsjdk.samtools.cram.structure.Block

Write the block out to the the specified OutputStream.

write(FastqRecord) - Method in class htsjdk.samtools.fastq.BasicFastqWriter
 
write(FastqRecord) - Method in interface htsjdk.samtools.fastq.FastqWriter
 
write(File) - Method in class htsjdk.samtools.metrics.MetricsFile

Writes out the metrics file to the supplied file.

write(Writer) - Method in class htsjdk.samtools.metrics.MetricsFile

Writes out the metrics file to the supplied writer.

write(T) - Method in class htsjdk.samtools.util.AbstractAsyncWriter

Public method for sub-classes or ultimately consumers to put an item into the queue
 to be written out.

write(char[], int, int) - Method in class htsjdk.samtools.util.AsciiWriter

All other Writer methods vector through this, so this is the only one that must be overridden.

write(byte[]) - Method in class htsjdk.samtools.util.BlockCompressedOutputStream

Writes b.length bytes from the specified byte array to this output stream.

write(byte[], int, int) - Method in class htsjdk.samtools.util.BlockCompressedOutputStream

Writes len bytes from the specified byte array starting at offset off to this output stream.

write(int) - Method in class htsjdk.samtools.util.BlockCompressedOutputStream

Writes the specified byte to this output stream.

write(File) - Method in class htsjdk.samtools.util.IntervalList

Writes out the list of intervals to the supplied file.

write(int) - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
 
write(byte[]) - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
 
write(byte[], int, int) - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
 
write(byte[]) - Method in class htsjdk.samtools.util.PositionalOutputStream
 
write(byte[], int, int) - Method in class htsjdk.samtools.util.PositionalOutputStream
 
write(int) - Method in class htsjdk.samtools.util.PositionalOutputStream
 
write(LittleEndianOutputStream) - Method in class htsjdk.tribble.index.AbstractIndex
 
write(File) - Method in class htsjdk.tribble.index.AbstractIndex
 
write(LittleEndianOutputStream) - Method in interface htsjdk.tribble.index.ChrIndex
 
write(LittleEndianOutputStream) - Method in interface htsjdk.tribble.index.Index

all indexes are writable to disk

write(File) - Method in interface htsjdk.tribble.index.Index

Writes the index into a file.

write(LittleEndianOutputStream) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
 
write(LittleEndianOutputStream) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
 
write(File) - Method in class htsjdk.tribble.index.tabix.TabixIndex

Writes the index with BGZF.

write(LittleEndianOutputStream) - Method in class htsjdk.tribble.index.tabix.TabixIndex
 
write(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
write(byte[], int, int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
write(int, OutputStream) - Method in enum htsjdk.variant.bcf2.BCF2Type
 
write(OutputStream) - Method in class htsjdk.variant.bcf2.BCFVersion

Write out the BCF magic information indicating this is a BCF file with corresponding major and minor versions

WRITE_BUFFER_INITIAL_SIZE - Static variable in class htsjdk.variant.variantcontext.writer.BCF2Encoder
 
writeAlignment(SAMRecord) - Method in class htsjdk.samtools.CRAMContainerStreamWriter

Write an alignment record.

writeAlignment(SAMRecord) - Method in class htsjdk.samtools.CRAMFileWriter

Write an alignment record.

writeAlignment(SAMRecord) - Method in class htsjdk.samtools.SAMFileWriterImpl

Writes the record to disk.

writeAlignment(SAMRecord) - Method in class htsjdk.samtools.SAMTextWriter

Write the record.

writeBasedOnFeatureFile(File) - Method in class htsjdk.tribble.index.AbstractIndex
 
writeBasedOnFeatureFile(File) - Method in interface htsjdk.tribble.index.Index

Write an appropriately named and located Index file based on the name and location of the featureFile.

writeBasedOnFeatureFile(File) - Method in class htsjdk.tribble.index.tabix.TabixIndex

Writes to a file with appropriate name and directory based on feature file.

writeBoolean(boolean) - Method in class htsjdk.samtools.util.BinaryCodec

Writes a boolean (1 byte) to the output buffer

writeBoolean(boolean) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
writeByte(byte) - Method in class htsjdk.samtools.util.BinaryCodec

Writes a byte to the output buffer

writeByte(int) - Method in class htsjdk.samtools.util.BinaryCodec
 
writeByte(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
writeBytes(byte[]) - Method in class htsjdk.samtools.util.BinaryCodec

Writes a byte array to the output buffer

writeBytes(byte[], int, int) - Method in class htsjdk.samtools.util.BinaryCodec
 
writeBytes(String) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
writeChar(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
writeContainer(Version, Container, OutputStream) - Static method in class htsjdk.samtools.cram.structure.ContainerIO

Writes a complete Container with it's header to a OutputStream.

writeContainerHeader(int, Container, OutputStream) - Static method in class htsjdk.samtools.cram.structure.ContainerIO

Writes a Container header information to a OutputStream.

writeCramHeader(CramHeader, OutputStream) - Static method in class htsjdk.samtools.cram.build.CramIO

Writes CRAM header into the specified OutputStream.

writeData(T) - Method in interface htsjdk.samtools.cram.encoding.writer.DataWriter

Write some data out.

writeDouble(double) - Method in class htsjdk.samtools.util.BinaryCodec

Write a double (8 bytes) to the output stream

writeDouble(double) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
writeFieldKey(BCF2Encoder) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

Write the field key (dictionary offset and type) into the BCF2Encoder stream

writeFloat(float) - Method in class htsjdk.samtools.util.BinaryCodec

Write a float (4 bytes) to the output stream

writeFloat(float) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
writeHeader(Version, OutputStream, SAMFileHeader, String) - Static method in class htsjdk.samtools.cram.build.CramIO

Write a CRAM File header and a SAM Header to an output stream.

writeHeader(SAMFileHeader) - Method in class htsjdk.samtools.CRAMContainerStreamWriter

Write a CRAM file header and SAM header to the stream.

writeHeader(String) - Method in class htsjdk.samtools.CRAMFileWriter
 
writeHeader(String) - Method in class htsjdk.samtools.SAMFileWriterImpl

Write the header to disk.

writeHeader(String) - Method in class htsjdk.samtools.SAMTextWriter

Write the header text.

writeHeader(VCFHeader) - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
 
writeHeader(VCFHeader) - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter
 
writeIndex(OutputStream) - Method in class htsjdk.samtools.cram.CRAIIndex

Write out the index to an output stream;

writeIndex(SeekableStream, OutputStream) - Static method in class htsjdk.samtools.CRAMCRAIIndexer

Generate and write a CRAI index to an output stream from a CRAM input stream

writeIndex(Index, File) - Static method in class htsjdk.tribble.index.IndexFactory

Deprecated.
use Index.write(File) instead


writeInt(int) - Method in class htsjdk.samtools.util.BinaryCodec

Write a 32-bit int to the output stream

writeInt(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
writeInt32(int, OutputStream) - Static method in class htsjdk.samtools.cram.io.CramInt

Write int value to OutputStream encoded as CRAM int data type.

writeInt32(int) - Static method in class htsjdk.samtools.cram.io.CramInt

Write int value to OutputStream encoded as CRAM int data type.

writeLong(long) - Method in class htsjdk.samtools.util.BinaryCodec

Write a 64-bit long to the output stream

writeLong(long) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
Writer - Class in htsjdk.samtools.cram.encoding.writer
 
Writer() - Constructor for class htsjdk.samtools.cram.encoding.writer.Writer
 
writeShort(short) - Method in class htsjdk.samtools.util.BinaryCodec

Write a 16-bit short to output stream

writeShort(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
 
writeSingleValue(byte, Object, boolean) - Static method in class htsjdk.samtools.cram.structure.ReadTag
 
writeString(String, boolean, boolean) - Method in class htsjdk.samtools.util.BinaryCodec

Writes a string to the buffer as ASCII bytes

writeString(String) - Method in class htsjdk.tribble.util.LittleEndianOutputStream

Srite a string as a null terminated byte array.

writeTable(PrintStream) - Method in class htsjdk.tribble.index.linear.LinearIndex

Code to convert linear index to a text table for analysis

writeTag(short, Object, boolean) - Method in class htsjdk.samtools.BinaryTagCodec

Write the given tag name and value to disk.

writeTime - Variable in class htsjdk.samtools.cram.structure.Container
 
writeToStream(OutputStream) - Method in class htsjdk.samtools.cram.CRAIEntry

Serialize the entry to a CRAI index stream.

writeUByte(short) - Method in class htsjdk.samtools.util.BinaryCodec

Write an 8-bit unsigned byte.

writeUInt(long) - Method in class htsjdk.samtools.util.BinaryCodec

Write a 32-bit unsigned int.

writeUnsignedITF8(int, OutputStream) - Static method in class htsjdk.samtools.cram.io.ITF8

Writes an unsigned (32 bit) integer to an OutputStream encoded as ITF8.

writeUnsignedITF8(int) - Static method in class htsjdk.samtools.cram.io.ITF8

Writes an unsigned (32 bit) integer to a byte new array encoded as ITF8.

writeUnsignedITF8(int, ByteBuffer) - Static method in class htsjdk.samtools.cram.io.ITF8

Writes an unsigned (32 bit) integer to an OutputStream encoded as ITF8.

writeUnsignedLTF8(long, OutputStream) - Static method in class htsjdk.samtools.cram.io.LTF8

Writes an unsigned long value to the output stream.

writeUShort(int) - Method in class htsjdk.samtools.util.BinaryCodec

Write a 16-bit unsigned short.

written - Variable in class htsjdk.tribble.util.LittleEndianOutputStream
 




X

XF - Static variable in class htsjdk.samtools.ReservedTagConstants

The Four54 edit string of 454 cafie and homopolymer corrections

XN - Static variable in class htsjdk.samtools.ReservedTagConstants

Present and set to 1 if a read is a noise read.

XQ - Static variable in class htsjdk.samtools.ReservedTagConstants

The sum of the mismatched qualities.

XS - Static variable in class htsjdk.samtools.ReservedTagConstants

The original sequence before 454 cafie and homopolymer correction

XT - Static variable in class htsjdk.samtools.ReservedTagConstants

The name of an attribute which stores the 1-based index of the start of
 sequence within a read (in original orientation) that should be clipped
 or trimmed before alignment and downstream use.

xz(byte[]) - Static method in class htsjdk.samtools.cram.io.ExternalCompression

Compress a byte array into XZ blob.





Z

ZERO_B_EOF_MARKER - Static variable in class htsjdk.samtools.cram.build.CramIO

The 'zero-B' EOF marker as per CRAM specs v2.1.

ZERO_BASED - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
 
ZERO_F_EOF_MARKER - Static variable in class htsjdk.samtools.cram.build.CramIO

The zero-F EOF marker as per CRAM specs v3.0.


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