htsjdk.samtools.reference (htsjdk 2.18.2 API)

Interface Summary
Interface Description

ReferenceSequenceFile
An interface for working with files of reference sequences regardless of the file format being used.

Interface Summary
Interface	Description
ReferenceSequenceFile	An interface for working with files of reference sequences regardless of the file format being used.

Class Summary
Class	Description
BlockCompressedIndexedFastaSequenceFile	A block-compressed FASTA file driven by an index for fast lookups.
FastaSequenceFile	Implementation of ReferenceSequenceFile for reading from FASTA files.
FastaSequenceIndex	Reads/writes a fasta index file (.fai), as generated by `samtools faidx`.
FastaSequenceIndexCreator	Static methods to create an `FastaSequenceIndex`.
FastaSequenceIndexEntry	Hold an individual entry in a fasta sequence index file.
IndexedFastaSequenceFile	A fasta file driven by an index for fast, concurrent lookups.
ReferenceSequence	Wrapper around a reference sequence that has been read from a reference file.
ReferenceSequenceFileFactory	Factory class for creating ReferenceSequenceFile instances for reading reference sequences store in various formats.
ReferenceSequenceFileWalker	Manages a ReferenceSequenceFile.
SamLocusAndReferenceIterator	Iterator that traverses a SAM File and a ReferenceFile, accumulating information on a per-locus basis.
SamLocusAndReferenceIterator.SAMLocusAndReference	Small class to hold together a `SamLocusIterator.LocusInfo` and the reference base over that locus.

Package htsjdk.samtools.reference