Skip to content
This repository has been archived by the owner on Jun 3, 2021. It is now read-only.
/ htslib Public archive
forked from SelfHacked/htslib

C library for high-throughput sequencing data formats

License

Notifications You must be signed in to change notification settings

selfdecode/htslib

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Build Status Build status Github All Releases

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.

HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent.

This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and the bgzip compression utility.

Building HTSlib

See INSTALL for complete details. Release tarballs contain generated files that have not been committed to this repository, so building the code from a Git repository requires extra steps:

autoheader     # If using configure, generate the header template...
autoconf       # ...and configure script (or use autoreconf to do both)
./configure    # Optional but recommended, for choosing extra functionality
make
make install

About

C library for high-throughput sequencing data formats

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages

  • C 88.5%
  • C++ 4.0%
  • Perl 2.7%
  • Makefile 1.4%
  • M4 1.3%
  • Roff 1.2%
  • Other 0.9%