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htslib

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    • user avatar
    Add -l / --compress-level option to bgzip
    Nathan T. Weeks authored and Rob Davies committed
    effcb1e1
    History
    user avatar effcb1e1
    History
    Name Last commit Last update
    cram
    htslib
    m4
    os
    test
    .appveyor.yml
    .gitattributes
    .gitignore
    .travis.yml
    INSTALL
    LICENSE
    Makefile
    NEWS
    README
    README.md
    bcf_sr_sort.c
    bcf_sr_sort.h
    bgzf.c
    bgzip.c
    config.mk.in
    configure.ac
    errmod.c
    faidx.5
    faidx.c
    hfile.c
    hfile_gcs.c
    hfile_internal.h
    hfile_libcurl.c
    hfile_net.c
    hfile_s3.c
    hts.c
    hts_internal.h
    hts_os.c
    htsfile.1
    htsfile.c
    htslib.mk
    htslib.pc.in
    htslib_vars.mk
    kfunc.c
    knetfile.c
    kstring.c
    md5.c
    multipart.c
    plugin.c
    probaln.c
    realn.c
    regidx.c
    sam.5
    sam.c
    synced_bcf_reader.c
    tabix.1
    tabix.c
    tbx.c
    textutils.c
    textutils_internal.h
    thread_pool.c
    thread_pool_internal.h
    vcf.5
    vcf.c
    vcf_sweep.c
    vcfutils.c
    version.sh
    README.md

    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, needed for choosing optional functionality
make
make install