# Package htsjdk.samtools.reference

package htsjdk.samtools.reference

Related Packages
Package
Description
htsjdk.samtools
Class
Description
BlockCompressedIndexedFastaSequenceFile
A block-compressed FASTA file driven by an index for fast lookups.
FastaReferenceWriter
Writes a FASTA formatted reference file.
FastaReferenceWriterBuilder
Buider for a `FastaReferenceWriter`
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.
ReferenceSequenceFile
An interface for working with files of reference sequences regardless of the file format being used.
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.