Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package libhts for openSUSE:Factory checked in at 2021-05-18 18:26:52 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/libhts (Old) and /work/SRC/openSUSE:Factory/.libhts.new.2988 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "libhts" Tue May 18 18:26:52 2021 rev:3 rq:893486 version:1.12 Changes: -------- --- /work/SRC/openSUSE:Factory/libhts/libhts.changes 2021-03-03 18:36:04.647422884 +0100 +++ /work/SRC/openSUSE:Factory/.libhts.new.2988/libhts.changes 2021-05-18 18:27:13.318759694 +0200 @@ -1,0 +2,47 @@ +Wed Apr 28 16:03:54 UTC 2021 - Ferdinand Thiessen <[email protected]> + +- Update to version 1.12: + * Added experimental CRAM 3.1 and 4.0 support. + * Added a general filtering syntax for alignment records in + SAM/BAM/CRAM readers. + * The knet networking code has been removed if favor of libcurl + * The old htslib/knetfile.h interfaces have been marked as deprecated. + * Added an introspection API for checking some of the capabilities + provided by HTSlib + * Made performance improvements to probaln_glocal method, which + speeds up mpileup BAQ calculations. + * Added a public method for constructing a BAM record from the + component pieces. + * Added two public methods, sam_parse_cigar and bam_parse_cigar, + as part of a small CIGAR API + * HTSlib, and the included htsfile program, will now recognise + the old RAZF compressed file format. Note that while the format + is detected, HTSlib is unable to read it. + * The S3 plugin now has options to force the address style. + It will recognise the addressing_style and host_bucket entries + in the respective AWS .credentials and s3cmd .s3cfg files. + * Fixed VCF #CHROM header parsing to only separate columns at tab + characters. + * Fixed a crash reported in bcf_sr_sort_set, which expects REF + to be present. + * Fixed a bcf synced reader bug when filtering with a region list, + and the first record for a chromosome had the same position as + the last record for the previous chromosome. + * Fixed a bug in the overlapping logic of mpileup, dealing with + iterating over CIGAR segments. + * Fixed a tabix bug that prevented setting the correct number of + lines to be skipped in a region file. + * Made bam_itr_next an alias for sam_itr_next, to prevent it from + crashing when working with htsFile pointers. + * Fixed once per outgoing multi-threaded block bgzf_idx_flush + assertion, to accommodate situations when a single record could + span multiple blocks. + * Fixed assumption of pthread_t being a non-structure, as + permitted by POSIX. + * Fixed the minimum offset of a BAI index bin, to account for + unmapped reads. + * Fixed the CRLF handling in sam_parse_worker method. + * Included unistd.h and errno.h directly in HTSlib files, as + opposed to including them indirectly, via third party code. + +------------------------------------------------------------------- Old: ---- htslib-1.11.tar.bz2 New: ---- htslib-1.12.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ libhts.spec ++++++ --- /var/tmp/diff_new_pack.zUyfCr/_old 2021-05-18 18:27:13.794757631 +0200 +++ /var/tmp/diff_new_pack.zUyfCr/_new 2021-05-18 18:27:13.798757614 +0200 @@ -17,7 +17,7 @@ Name: libhts -Version: 1.11 +Version: 1.12 Release: 0 %define sonum 3 Summary: C library for high-throughput sequencing data formats ++++++ htslib-1.11.tar.bz2 -> htslib-1.12.tar.bz2 ++++++ ++++ 45643 lines of diff (skipped)
