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.