Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package libhts for openSUSE:Factory checked in at 2024-07-28 17:20:21 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/libhts (Old) and /work/SRC/openSUSE:Factory/.libhts.new.1882 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "libhts" Sun Jul 28 17:20:21 2024 rev:7 rq:1189980 version:1.20 Changes: -------- --- /work/SRC/openSUSE:Factory/libhts/libhts.changes 2024-01-03 14:53:27.460682632 +0100 +++ /work/SRC/openSUSE:Factory/.libhts.new.1882/libhts.changes 2024-07-28 17:20:48.135051337 +0200 @@ -1,0 +2,48 @@ +Mon Jul 15 12:17:55 UTC 2024 - jun wang <jgwang@suse.com> + +- Update to version 1.20 + * When working on named files, bgzip now sets the modified and + access times of the output files it makes to match those of + the corresponding input + * It's now possible to use a -o option to specify the output + file name in bgzip + * Improved error faidx error messages + * Faster reading of SAM array (type "B") tags. These often turn + up in ONT and PacBio data + * Improved validity checking of base modification tags + * mpileup overlap removal now works where one read has a + deletion + * The S3 plugin can now find buckets via S3 access point aliases + * Added a --threads option (and -@ short option) to tabix + * tabix can now index Graph Alignment Format (GAF) files + * Security fix: Prevent possible heap overflow in + cram_encode_aux() on bad RG:Z tags + * Security fix: Prevent attempts to call a NULL pointer if + certain URL schemes are used in CRAM @SQ UR: tags + * Security fix: Fixed a bug where following certain AWS S3 + redirects could downgrade the connection from TLS + (i.e. https://) to unencrypted http://. This could happen when + using path-based URLs and AWS_DEFAULT_REGION was set to a + region other that the one where the data was stored + * Fixed arithmetic overflow when loading very long references + for CRAM + * Fixed faidx and CRAM reference look-ups on compressed fasta + where the .fai index file was present, but the .gzi index of + compressed offsets was not + * Fixed BCF indexing on-the-fly bug which produced invalid + indexes when using multiple compression threads + * Ensure that pileup destructors are called by + bam_plp_destroy(), to prevent memory leaks + * Ensure on-the-fly index timestamps are always older than the + data file. Previously the files could be closed out of order, + leading to warnings being printed when using the index + * To prevent data corruption when reading (strictly invalid) + VCF files with duplicated FORMAT tags, all but the first copy + of the data associated with the tag are now dropped with a + warning + * Fixed a bug introduced in release 1.19 (PR #1689) which broke + variant record data if it tried to remove an over-long tag + * Changed error to warning when complaining about use of the CG + tag in SAM or CRAM files + +------------------------------------------------------------------- Old: ---- htslib-1.19.tar.bz2 New: ---- htslib-1.20.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ libhts.spec ++++++ --- /var/tmp/diff_new_pack.iwEUFT/_old 2024-07-28 17:20:48.591069560 +0200 +++ /var/tmp/diff_new_pack.iwEUFT/_new 2024-07-28 17:20:48.595069720 +0200 @@ -20,7 +20,7 @@ %define htscodecsminversion 1.6.0 Name: libhts -Version: 1.19 +Version: 1.20 Release: 0 %define sonum 3 Summary: C library for high-throughput sequencing data formats ++++++ htslib-1.19.tar.bz2 -> htslib-1.20.tar.bz2 ++++++ ++++ 4473 lines of diff (skipped)