Package htsjdk.samtools.reference
package htsjdk.samtools.reference
-
ClassDescriptionA block-compressed FASTA file driven by an index for fast lookups.Writes a FASTA formatted reference file.Buider for a
FastaReferenceWriter
Implementation of ReferenceSequenceFile for reading from FASTA files.Reads/writes a fasta index file (.fai), as generated by `samtools faidx`.Static methods to create anFastaSequenceIndex
.Hold an individual entry in a fasta sequence index file.A fasta file driven by an index for fast, concurrent lookups.Wrapper around a reference sequence that has been read from a reference file.An interface for working with files of reference sequences regardless of the file format being used.Factory class for creating ReferenceSequenceFile instances for reading reference sequences store in various formats.Manages a ReferenceSequenceFile.Iterator that traverses a SAM File and a ReferenceFile, accumulating information on a per-locus basis.Small class to hold together aSamLocusIterator.LocusInfo
and the reference base over that locus.