Package htsjdk.samtools.reference

Interface Summary

ReferenceSequenceFile

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

Class Summary

FastaSequenceFile	Implementation of ReferenceSequenceFile for reading from FASTA files.
FastaSequenceIndex	Reads a fasta index file (.fai), as generated by `samtools faidx`.
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.