C library for high-throughput sequencing data formats. This is the repository for any necessary gamgee-specific changes.
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doc
htslib
misc
test
.gitignore
Makefile
README.md
abreak.c
bam2bed.c
bam2fq.c
bamidx.c
bamshuf.c
bcfidx.c
main.c
samview.c
tabix.c
vcfcheck.c
vcffilter.c
vcfgtcheck.c
vcfisec.c
vcfmerge.c
vcfnorm.c
vcfquery.c
vcfview.c

README.md

HTSlib is an experimental implementation of a unified C library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. The library is contained in the htslib subdirectory. Each command-line tool is implemented in one C source code file in the toplevel directory. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.

HTSlib implements a generalized BAM index. The command-line tools bamidx and tabix write the old index by default, but can also write a new 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.

HTSlib is unfinished. It has not been tested on large-scale real data. Some useful APIs are missing.