Indexer of BAM.

Converters between equivalent formats: SAM/BAM and FASTA/TwoBit.

Functions to remove duplications.

Provides algorithms for calculating simple depth of coverage.

Alpha - subject to change.
Generator of a FASTA sequence dictionary file.

Indexer of FASTA.

Level analyzer of alignments in BAM.

Functions to normalize the SAM/BAM format.

Functions to calculate pileup from the BAM.

Sorter of the SAM/BAM format alignments.

Indexer of VCF/BCF.

Common vars.

Parser for a BAM index file.

Functions to read and write the BED (Browser Extensible Data) format. See
http://genome.ucsc.edu/FAQ/FAQformat#format1 for the detail BED specifications.

Functions to read the bigWig format. See https://genome.ucsc.edu/goldenpath/help/bigWig.html
and https://github.com/ucscGenomeBrowser/kent for the detail bigWig
specifications.

Alpha - subject to change. Provides functions for reading from a CRAM file.

Basic I/O of CSI:Coordinate Sorted Index files.

Functions to read and write the FASTQ format.

Protocols of reader/writer for various file formats.

Functions to read and write the SAM (Sequence Alignment/Map) format and BAM
(its binary equivalent). See https://samtools.github.io/hts-specs/ for the
detail SAM/BAM specifications.

Functions to read and write formats representing sequences such as FASTA and
TwoBit.

Alpha - subject to change.
Reader of a TABIX format file.

I/O utilities.

Functions to read and write the VCF (Variant Call Format) format and BCF (its
binary equivalent). See https://samtools.github.io/hts-specs/ for the detail
VCF/BCF specifications.

Functions to read and write the WIG (Wiggle) format. See
https://genome.ucsc.edu/goldenpath/help/wiggle.html for the detail WIG
specifications.

General utilities.

Utilities for handling chromosome name.

Data structures for interval queries.

Utility functions for manipulating chromosomal regions.

Utilities for conversions between chromosomal positions and whole-genome
positions.