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 retur