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