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cram
cram
 
 
htscodecs
htscodecs
 
 
htslib
htslib
 
 
m4
m4
 
 
os
os
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
bcf_sr_sort.c
bcf_sr_sort.c
 
 
bcf_sr_sort.h
bcf_sr_sort.h
 
 
bgzf.c
bgzf.c
 
 
build_lib.sh
build_lib.sh
 
 
config.mk.in
config.mk.in
 
 
configure.ac
configure.ac
 
 
errmod.c
errmod.c
 
 
faidx.c
faidx.c
 
 
header.c
header.c
 
 
header.h
header.h
 
 
hfile.c
hfile.c
 
 
hfile_gcs.c
hfile_gcs.c
 
 
hfile_internal.h
hfile_internal.h
 
 
hfile_libcurl.c
hfile_libcurl.c
 
 
hfile_s3.c
hfile_s3.c
 
 
hfile_s3_write.c
hfile_s3_write.c
 
 
hts.c
hts.c
 
 
hts_expr.c
hts_expr.c
 
 
hts_internal.h
hts_internal.h
 
 
hts_os.c
hts_os.c
 
 
htscodecs.mk
htscodecs.mk
 
 
htscodecs.mk.in
htscodecs.mk.in
 
 
htscodecs_bundled.mk
htscodecs_bundled.mk
 
 
htscodecs_external.mk
htscodecs_external.mk
 
 
htslib-s3-plugin.7
htslib-s3-plugin.7
 
 
htslib.mk
htslib.mk
 
 
htslib.pc.in
htslib.pc.in
 
 
htslib_vars.mk
htslib_vars.mk
 
 
kfunc.c
kfunc.c
 
 
kstring.c
kstring.c
 
 
md5.c
md5.c
 
 
multipart.c
multipart.c
 
 
plugin.c
plugin.c
 
 
probaln.c
probaln.c
 
 
realn.c
realn.c
 
 
regidx.c
regidx.c
 
 
region.c
region.c
 
 
sam.c
sam.c
 
 
sam_internal.h
sam_internal.h
 
 
synced_bcf_reader.c
synced_bcf_reader.c
 
 
tbx.c
tbx.c
 
 
textutils.c
textutils.c
 
 
textutils_internal.h
textutils_internal.h
 
 
thread_pool.c
thread_pool.c
 
 
thread_pool_internal.h
thread_pool_internal.h
 
 
vcf.c
vcf.c
 
 
vcf_sweep.c
vcf_sweep.c
 
 
vcfutils.c
vcfutils.c
 
 
version.sh
version.sh
 
 

README.md

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 may contain generated files that have not been committed to this repository, so building the code from a Git repository requires extra steps:

autoreconf -i  # Build the configure script and install files it uses
./configure    # Optional but recommended, for choosing extra functionality
make
make install

For example, if linking with libdeflate is desired (to speed up zlib compression/decompression), and the installation prefix should be /ccb/sw/ (which could also be the prefix of libdeflate installation in this exmple), the following configure command can be used:

CPPFLAGS=-I/ccb/sw/include LDFLAGS=-L/ccb/sw/lib \
./configure --prefix=/ccb/sw --with-libdeflate