C library for high-throughput sequencing data formats
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 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.
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Source Files
| Filename | Size | Changed |
|---|---|---|
| baselibs.conf | 0000000098 98 Bytes | |
| htslib-1.10.2.tar.bz2 | 0001306320 1.25 MB | |
| libhts.changes | 0000011205 10.9 KB | |
| libhts.spec | 0000005906 5.77 KB |
Revision 6 (latest revision is 18)
Pierre Bonamy (flyos)
accepted
request 770317
from
Todd R (TheBlackCat)
(revision 6)
- Update to release 1.10.2
* This is a release fix that corrects minor inconsistencies discovered in
previous deliverables.
- Update to release 1.10.1
* The support for 64-bit coordinates in VCF brought problems for files
not conforming to VCF/BCF specification. While previous versions would
make out-of-range values silently overflow creating nonsense values
but parseable file, the version 1.10 would silently create an invalid BCF.
- Update to release 1.10
+ Brief summary
* Addition of support for references longer than 2Gb (NB: SAM and VCF
formats only, not their binary counterparts). This may need changes
in code using HTSlib. See README.large_positions.md for more information.
* Added a SAM header API.
* Major speed up to SAM reading and writing. This also now supports
multi-threading.
* We can now auto-index on-the-fly while writing a file. This also
includes to bgzipped SAM.gz.
* Overhaul of the S3 interface, which now supports version 4
signatures. This also makes writing to S3 work.
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