tabix - Generic indexer for TAB-delimited genome position files from the HTSlib project
||openSUSE Leap 15.0
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.
- Add the Science repository:
# zypper addrepo http://widehat.opensuse.org/opensuse/repositories/science/openSUSE_Leap_15.0/ science
- Install tabix rpm package:
# zypper install tabix
2018-09-06 - email@example.com
- Update to 1.9
* If `./configure` fails, `make` will stop working until either configure
is re-run successfully, or `make distclean` is used. This makes
configuration failures more obvious. (#711, thanks to John Marshall)
* The default SAM version has been changed to 1.6. This is in line with the
latest version specification and indicates that HTSlib supports the
CG tag used to store long CIGAR data in BAM format.
* bgzip integrity check option '--test' (#682, thanks to @sd4B75bJ, @jrayner)
* Faidx can now index fastq files as well as fasta. The fastq index adds
an extra column to the `.fai` index which gives the offset to the quality
values. New interfaces have been added to `htslib/faidx.h` to read the
fastq index and retrieve the quality values. It is possible to open
a fastq index as if fasta (only sequences will be returned), but not
the other way round. (#701)
* New API interfaces to add or update integer, float and array aux tags. (#694)
* Add `level=<number>` option to `hts_set_opt()` to allow the compression
level to be set. Setting `level=0` enables uncompressed output. (#715)
* Improved bgzip error reporting.
* Better error reporting when CRAM reference files can't be opened. (#706)
* Fixes to make tests work properly on Windows/MinGW - mainly to handle
line ending differences. (#716)
* Efficiency improvements:
- Small speed-up for CRAM indexing.
- Reduce the number of unnecessary wake-ups in the thread pool. (#703)
- Avoid some memory copies when writing data, notably for uncompressed
BGZF output. (#703)
* Bug fixes:
- Fix multi-region iterator bugs on CRAM files. (#684)
- Fixed multi-region iterator bug that caused some reads to be skipped
incorrectly when reading BAM files. (#687)
- Fixed synced_bcf_reader() bug when reading contigs multiple times. (#691,
reported by @freeseek)
- Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary
when removing samples. (#692, reported by @freeseek)
- Fixed bug where the VCF record ref length was calculated incorrectly
if an INFO END tag was present. (71b00a)
- Fixed warnings found when compiling with gcc 8.1.0. (#700)
- sam_hdr_read() and sam_hdr_write() will now return an error code
if passed a NULL file pointer, instead of crashing.
- Fixed possible negative array look-up in sam_parse1() that somehow
escaped previous fuzz testing. (#731, reported by @fCorleone)
- Fixed bug where cram range queries could incorrectly report an error
when using multiple threads. (#734, reported by Brent Pedersen)
- Fixed very rare rANS normalisation bug that could cause an assertion
failure when writing CRAM files. (#739, reported by @carsonhh)