Revisions of libhts
buildservice-autocommit
accepted
request 1136409
from
Pierre Bonamy (flyos)
(revision 18)
baserev update by copy to link target
Pierre Bonamy (flyos)
accepted
request 1136374
from
Stefan Brüns (StefanBruens)
(revision 17)
- Update to version 1.19 Too many changes to list, for details see https://github.com/samtools/htslib/releases/tag/1.19 - Update to version 1.18 Too many changes to list, for details see https://github.com/samtools/htslib/releases/tag/1.18 - Update to version 1.17 Too many changes to list, for details see https://github.com/samtools/htslib/releases/tag/1.17
buildservice-autocommit
accepted
request 1002325
from
Pierre Bonamy (flyos)
(revision 16)
baserev update by copy to link target
Pierre Bonamy (flyos)
accepted
request 1002209
from
Stefan Brüns (StefanBruens)
(revision 15)
- Update to version 1.16 * Make hfile_s3 refresh AWS credentials on expiry in order to make HTSlib work better with AWS IAM credentials, which have a limited lifespan. * Allow BAM headers between 2GB and 4GB in size once more. * Improve error message when failing to load an index. * Permit MM (base modification) tags containing . and ? suffixes. * Warn if spaces instead of tabs are detected in a VCF file to prevent confusion. * Add an sclen filter expression keyword. * Improve error messages for CRAM reference mismatches. * Expose more of the CRAM API and add new functionality to extract the reference from a CRAM file. * Improvements to the implementation of embedded references in CRAM where no external reference is specified. * The CRAM writer now allows alignment records with RG:Z: aux tags that don't have a corresponding @RG ID in the file header. * Set tab delimiter in man page for tabix GFF3 sort. * When using libdeflate, the 1...9 scale of BGZF compression levels is now remapped to the 1...12 range used by libdeflate instead of being passed directly. * The VCF variant API has been extended so that it can return separate flags for INS and DEL variants as well as the existing INDEL one. * The missing, but trivial, le_to_u8() function has been added to hts_endian. * bcf_format_gt() now works properly on big-endian platforms. * Update htscodecs to version 1.3.0 for new SIMD code + various fixes. * Detect ARM Neon support and only build appropriate SIMD object files. * make print-config now reports extra CFLAGS that are needed to build the SIMD parts of htscodecs. * Fixed some Makefile dependency issues for the check/test targets and plugins. * Fix bug when reading position -1 in BCF (0 in VCF), which is used to indicate telomeric regions. * Various bugs and quirks have been fixed in the filter expression engine, mostly related to the handling of absent tags, and the is_true flag. * Fix buffer overrun in bam_plp_insertion_mod. * Remove limit of returned size from fai_retrieve(). * Cap hts_getline() return value at INT_MAX. * Fix breakend detection and test bcf_set_variant_type(). * Prevent arrays of BCF_BT_NULL values found in BCF files from causing bcf_fmt_array() to call exit() as the type is unsupported. * Improved detection of fasta and fastq files that have very long comments following identifiers. * Fixed a SEGV triggered by giving a SAM file to samtools import.
buildservice-autocommit
accepted
request 974395
from
Ferdinand Thiessen (susnux)
(revision 14)
baserev update by copy to link target
Pierre Bonamy (flyos)
accepted
request 971255
from
Ferdinand Thiessen (susnux)
(revision 13)
Update to version 1.15.1
buildservice-autocommit
accepted
request 893486
from
Pierre Bonamy (flyos)
(revision 12)
baserev update by copy to link target
Pierre Bonamy (flyos)
accepted
request 889072
from
Ferdinand Thiessen (susnux)
(revision 11)
Update to version 1.12
buildservice-autocommit
accepted
request 876540
from
Dirk Stoecker (dstoecker)
(revision 10)
baserev update by copy to link target
Dirk Stoecker (dstoecker)
accepted
request 873586
from
jun wang (jgwang)
(revision 9)
Update to version 1.11
Dominique Leuenberger (dimstar_suse)
accepted
request 773222
from
Todd R (TheBlackCat)
(revision 8)
initialized devel package after accepting 773222
Pierre Bonamy (flyos)
accepted
request 773174
from
Todd R (TheBlackCat)
(revision 7)
- Include baselibs.conf as source file. - Update baselibs.conf.
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.
Pierre Bonamy (flyos)
accepted
request 633580
from
Pierre Bonamy (flyos)
(revision 5)
- 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)
Pierre Bonamy (flyos)
committed
(revision 4)
Pierre Bonamy (flyos)
accepted
request 622254
from
Pierre Bonamy (flyos)
(revision 3)
- Update to 1.8 - Better formatting of the descriptions - Spec file cleaned up using spec-cleaner
Matthias Mailänder (Mailaender)
accepted
request 393855
from
Pierre Bonamy (flyos)
(revision 1)
Removed _service
Displaying all 18 revisions