Package htsjdk.samtools

Interface Summary

Interface	Description
BAMIndex	A basic interface for querying BAM indices.
BinningIndexBuilder.FeatureToBeIndexed	coordinates are 1-based, inclusive
BrowseableBAMIndex	An index interface with additional functionality for querying and inspecting the structure of a BAM index.
CoordinateSortedPairInfoMap.Codec<KEY,REC>	Client must implement this class, which defines the way in which records are written to and read from file.
CustomReaderFactory.ICustomReaderFactory	Interface to be implemented by custom factory classes that register themselves with this factory and are loaded dynamically.
SAMFileSpan	A interface representing a collection of (possibly) discontinuous segments in the BAM file, possibly representing the results of an index query.
SAMFileWriter	Interface for SAMText and BAM file writers.
SamReader	Describes functionality for objects that produce SAMRecords and associated information.
SamReader.Indexing	Facet for index-related operations.
SamReader.PrimitiveSamReader	The minimal subset of functionality needed for a SAMRecord data source.
SAMRecordComparator	Interface for comparators that define the various SAM sort orders.
SAMRecordFactory	Factory interface which allows plugging in of different classes for generating instances of SAMRecord and BAMRecord when reading from SAM/BAM files.
SAMRecordIterator	A general interface that adds functionality to a CloseableIterator of SAMRecords.

Class Summary

Class	Description
AbstractBAMFileIndex	Provides basic, generic capabilities to be used reading BAM index files.
AbstractSAMHeaderRecord	Base class for the various concrete records in a SAM header, providing uniform access to the attributes.
AlignmentBlock	Represents the contiguous alignment of a subset of read bases to a reference sequence.
BamFileIoUtils
BAMFileSpan	An ordered list of chunks, capable of representing a set of discontiguous regions in the BAM file.
BAMIndexer	Class for both constructing BAM index content and writing it out.
BAMIndexMetaData	Metadata about the bam index contained within the bam index.
BamIndexValidator	Class to validate (at two different levels of thoroughness) the index for a BAM file.
BAMQueryMultipleIntervalsIteratorFilter	Filters out records that do not match any of the given intervals and query type.
BAMRecord	Wrapper class for binary BAM records.
BAMRecordCodec	Class for translating between in-memory and disk representation of BAMRecord.
Bin	An individual bin in a BAM file.
BinaryTagCodec	Converter between disk and in-memory representation of a SAMRecord tag.
BinList	Provides a list of all bins which could exist in the BAM file.
BinningIndexBuilder	Builder for a BinningIndexContent object.
BinningIndexContent	In-memory representation of the binning index for a single reference.
BinningIndexContent.BinList	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
Chunk	A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index.
Cigar	A list of CigarElements, which describes how a read aligns with the reference.
CigarElement	One component of a cigar string.
CoordinateSortedPairInfoMap<KEY,REC>	Holds info about a mate pair for use when processing a coordinate sorted file.
CRAMBAIIndexer	Class for both constructing BAM index content and writing it out.
CRAMContainerStreamWriter	Class for writing SAMRecords into a series of CRAM containers on an output stream.
CRAMCRAIIndexer	Indexer for creating/reading/writing a CRAIIndex for a CRAM file/stream.
CRAMFileReader	BAMFileReader analogue for CRAM files.
CRAMFileWriter
CRAMIterator
CustomReaderFactory	Factory for creating custom readers for accessing API based resources, e.g.
Defaults	Embodies defaults for global values that affect how the SAM JDK operates.
DefaultSAMRecordFactory	Default factory for creating SAM and BAM records used by the SamReader classes.
DiskBasedBAMFileIndex	A class for reading BAM file indices, hitting the disk once per query.
DownsamplingIterator	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.
DownsamplingIteratorFactory	A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while meeting various criteria.
DuplicateScoringStrategy	This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate during duplicate marking (see MarkDuplicates).
DuplicateSet	Stores a set of records that are duplicates of each other.
DuplicateSetIterator	An iterator of sets of duplicates.
FixBAMFile
GenomicIndexUtil	Constants and methods used by BAM and Tribble indices
LinearIndex	The linear index associated with a given reference in a BAM index.
MergingSamRecordIterator	Provides an iterator interface for merging multiple underlying iterators into a single iterable stream.
NotPrimarySkippingIterator	Wrapper around SAMRecord iterator that skips over non-primary elements.
QueryInterval	Interval relative to a reference, for querying a BAM file.
ReservedTagConstants	Constants for tags used in our SAM/BAM files
SAMBinaryTagAndUnsignedArrayValue	Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because signedness cannot be determined by introspection of value.
SAMBinaryTagAndValue	Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
SAMFileHeader	Header information from a SAM or BAM file.
SAMFileHeader.PgIdGenerator	Little class to generate program group IDs
SamFileHeaderMerger	Merges SAMFileHeaders that have the same sequences into a single merged header object while providing read group translation for cases where read groups clash across input headers.
SamFiles
SAMFileSource	Represents the origin of a SAM record.
SamFileValidator	Validates SAM files as follows: checks sam file header for sequence dictionary checks sam file header for read groups for each sam record reports error detected by SAMRecord.isValid() validates NM (nucleotide differences) exists and matches reality validates mate fields agree with data in the mate record
SamFileValidator.ValidationMetrics
SAMFileWriterFactory	Create a writer for writing SAM, BAM, or CRAM files.
SAMFileWriterImpl	Base class for implementing SAM writer with any underlying format.
SAMHeaderRecordComparator<T extends AbstractSAMHeaderRecord>	Provides ordering based on SAM header records' attribute values.
SamInputResource	Describes a SAM-like resource, including its data (where the records are), and optionally an index.
SAMLineParser	This class enables creation of a SAMRecord object from a String in SAM text format.
SamPairUtil	Utility methods for pairs of SAMRecords
SamPairUtil.SetMateInfoIterator	A class to iterate through SAMRecords and set mate information on the given records, and optionally set the mate cigar tag (true by default).
SAMProgramRecord	In-memory representation of @PG SAM header record.
SamReader.AssertingIterator
SamReader.PrimitiveSamReaderToSamReaderAdapter	Decorator for a SamReader.PrimitiveSamReader that expands its functionality into a SamReader, given the backing SamInputResource.
SamReader.ReaderImplementation	Internal interface for SAM/BAM/CRAM file reader implementations, as distinct from non-file-based readers.
SamReader.Type	Describes a type of SAM file.
SamReaderFactory	Describes the functionality for producing SamReader, and offers a handful of static generators.
SAMReadGroupRecord	Header information about a read group.
SAMRecord	Java binding for a SAM file record.
SAMRecord.SAMTagAndValue	Tag name and value of an attribute, for getAttributes() method.
SAMRecordCoordinateComparator	Comparator for sorting SAMRecords by coordinate.
SAMRecordDuplicateComparator	Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates).
SAMRecordQueryHashComparator	SAMRecord comparator that provides an ordering based on a hash of the queryname.
SAMRecordQueryNameComparator	Comparator for "queryname" ordering of SAMRecords.
SAMRecordSetBuilder	Factory class for creating SAMRecords for testing purposes.
SAMRecordUtil	Deprecated
SAMSequenceDictionary	Collection of SAMSequenceRecords.
SAMSequenceDictionaryCodec	"On the fly" codec SAMSequenceDictionaryCodec.
SAMSequenceRecord	Header information about a reference sequence.
SAMSortOrderChecker	Encapsulates simple check for SAMRecord order.
SamStreams	Utilities related to processing of InputStreams encoding SAM data
SAMTagUtil	Facility for converting between String and short representation of a SAM tag.
SAMTestUtil	Misc methods for SAM-related unit tests.
SAMTextHeaderCodec	Parser for a SAM text header, and a generator of SAM text header.
SAMTextWriter	Writer for text-format SAM files.
SAMTools	Command line utility for manipulating SAM/BAM files.
SAMUtils	Utilty methods.
SAMValidationError	Class that encapsulates a validation error message as well as a type code so that errors can be aggregated by type.
SecondaryOrSupplementarySkippingIterator	Wrapper around SAMRecord iterator that skips over secondary and supplementary elements.
SQTagUtil	Utility methods for encoding and decoding the SQ tag value of SAMRecord.
SRAFileReader
SRAIndex	Emulates BAM index so that we can request chunks of records from SRAFileReader Here is how it works: SRA allows reading of alignments by Reference position fast, so we divide our "file" range for alignments as a length of all references.
SRAIterator	SRA iterator which returns SAMRecords for requested list of chunks
SRAIterator.RecordRangeInfo	Describes record ranges info needed for emulating BAM index
TagValueAndUnsignedArrayFlag	CVO to use as a method return value.
TextCigarCodec	Convert between String and Cigar class representations of CIGAR.
TextTagCodec	Converter between SAM text representation of a tag, and in-memory Object representation.

Enum Summary

Enum	Description
BamIndexValidator.IndexValidationStringency
CigarOperator	The operators that can appear in a cigar string, and information about their disk representations.
DownsamplingIteratorFactory.Strategy	Describes the available downsampling strategies.
DuplicateScoringStrategy.ScoringStrategy
SAMFileHeader.GroupOrder
SAMFileHeader.SortOrder	Ways in which a SAM or BAM may be sorted.
SAMFlag	SAM flags as enum, to be used in GUI, menu, etc...
SamFlagField	This determines how flag fields are represented in the SAM file.
SamIndexes	A helper class to read BAI and CRAI indexes.
SamPairUtil.PairOrientation	The possible orientations of paired reads.
SamReaderFactory.Option	A collection of binary SamReaderFactory options.
SAMReadGroupRecord.PlatformValue
SAMTag	The standard tags for a SAM record that are defined in the SAM spec.
SAMValidationError.Severity
SAMValidationError.Type
SQTagUtil.SQBase	The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag.
ValidationStringency	How strict to be when reading a SAM or BAM, beyond bare minimum validation.

Exception Summary

Exception	Description
FileTruncatedException	Thrown when it is possible to detect that a SAM or BAM file is truncated.
SAMException
SAMFormatException	Thrown when a SAM file being read or decoded (text or binary) looks bad.
SAMTestUtil.SanityCheckFailedException	Indicates that a required sanity-check condition was not met.