Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package libhts for openSUSE:Factory checked in at 2021-03-03 18:35:52 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/libhts (Old) and /work/SRC/openSUSE:Factory/.libhts.new.2378 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "libhts" Wed Mar 3 18:35:52 2021 rev:2 rq:876540 version:1.11 Changes: -------- --- /work/SRC/openSUSE:Factory/libhts/libhts.changes 2020-02-11 22:24:54.047550987 +0100 +++ /work/SRC/openSUSE:Factory/.libhts.new.2378/libhts.changes 2021-03-03 18:36:04.647422884 +0100 @@ -1,0 +2,90 @@ +Fri Feb 19 01:11:53 UTC 2021 - Wang Jun <[email protected]> + +- Update to version 1.11: https://github.com/samtools/htslib/releases/tag/1.11 + * Features and Updates + - Support added for remote reference files. + - Added tabix --separate-regions option + - Added tabix --cache option to set a BGZF block cache size. + - Improved error checking in tabix and added a --verbosity option + - A note about the maximum chromosome length usable with TBI + indexes has been added to the tabix manual page. + - New method vcf_open_mode() changes the opening mode of a variant + file based on its file extension. + - The VCF parser has been made faster and easier to maintain. + - bcf_record_check() has been made faster + - The VCF parser now recognises the <NON_REF> symbolic allele produced by GATK. + - Support has been added for simultaneous reading of unindexed + VCF/BCF files when using the synced_bcf_reader interface. + - The VCF and BCF readers will now attempt to fix up invalid INFO/END tags + - The htsFile interface can now detect the crypt4gh encrypted format + - hts_srand48() now seeds the same POSIX-standard sequences of pseudo-random + numbers regardless of platform, including on OpenBSD where plain srand48() + produces a different cryptographically-strong non-deterministic sequence. + - Iterators now work with 64 bit positions. + - Improved the speed of range queries when using BAI indexes by making better + use of the linear index data included in the file. + - Alignments which consume no reference bases are now considered to have length 1. + - A bam_set_seqi() function to modify a single base in the BAM structure has been added. + - Writing SAM format is around 30% faster. + - Added sam_format_aux1() which converts a BAM aux tag to a SAM format string. + - bam_aux_update_str() no longer requires NUL-terminated strings. + - It is now possible to use external plug-ins in language bindings + that dynamically load HTSlib. + - bgzf_close(), and therefore hts_close(), will now return non-zero when + closing a BGZF handle on which errors have been detected. + - Added a special case to the kt_fisher_exact() test for when the table + probability is too small to be represented in a double. + - Improved error diagnostics in the CRAM decoder (#1042), BGZF (#1049), + the VCF and BCF readers (#1059), and the SAM parser (#1073). + - ks_resize() now allocates 1.5 times the requested size when it needs to + expand a kstring instead of rounding up to the next power of two. + * Bug fixes + - Fixed hfile_libcurl breakage when using libcurl 7.69.1 or later. + - Fixed overflows kroundup32() and kroundup_size_t() which caused them to return + zero when rounding up values where the most significant bit was set. + - Fixed missing return parameter value in idx_test_and_fetch(). + - Fixed crashes due to inconsistent selection between BGZF and plain (hFILE) + interfaces when reading files. + - Added and/or fixed byte swapping code for big-endian platforms. + - Fixed a problem with multi-threaded on-the-fly indexes which would occasionally + write virtual offsets pointing at the end of a BGZF block. + - In sam_hdr_create(), free newly allocated SN strings when encountering an error. + - Prevent double free in case of idx_test_and_fetch() failure. + - In the header, link a new PG line only to valid chains. Prevents an explosive + growth of PG lines on headers where PG lines are already present but not linked + together correctly. + - Also in the header, when calling sam_hdr_update_line(), update target arrays + only when the name or length is changed. + - Fixed buffer overflows in CRAM MD5 calculation triggered by files with invalid + compression headers, or files with embedded references that were one byte too short. + - Fix mpileup regression between 1.9 and 1.10 where overlap detection was incorrectly + skipped on reads where RNEXT, PNEXT and TLEN were set to the "unavailable" values + ("*", 0, 0 in SAM). + - kputs() now checks for null pointer in source string. + - Fix potential bcf_update_alleles() crash on 0 alleles. + - Added bcf_unpack() calls to some bcf_update functions to fix a bug where updates + made after a call to bcf_dup() could be lost. + - Error message typo "Number=R" instead of "Number=G" fixed in bcf_remove_allele_set(). + - Fixed crashes that could occur in BCF files that use IDX= header annotations to + create a sparse set of CHROM, FILTER or FORMAT indexes, and include records that + use one of the missing index values. + - Fixed potential integer overflows in the VCF parser and ensured that the total + length of FORMAT fields cannot go over 2Gbytes. + - Download index files atomically in idx_test_and_fetch(). This prevents corruption + when running parallel jobs on S3 files. + - The pileup constructor callback is now given the copy of the bam1_t struct made + by pileup instead of the original one passed to bam_plp_push(). + - Fixed possible error in code_sort() on negative CRAM Huffman code length. + - Fixed possible undefined shift in cram_byte_array_stop_decode_init(). + - Fixed a bug where range queries to the end of a given reference would return + incorrect results on CRAM files. + - Fixed an integer overflow in cram_read_slice(). + - Fixed a memory leak on failure in cram_decode_slice(). + - Fixed a regression which caused cram_transcode_rg() to fail, resulting in a + crash in "samtools cat" on CRAM files. + - Fixed an undersized string reallocation in the threaded SAM reader which caused + it to crash when reading SAM files with very long lines. Numerous memory allocation + checks have also been added. + + +------------------------------------------------------------------- Old: ---- htslib-1.10.2.tar.bz2 New: ---- htslib-1.11.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ libhts.spec ++++++ --- /var/tmp/diff_new_pack.VrbZs8/_old 2021-03-03 18:36:05.231423303 +0100 +++ /var/tmp/diff_new_pack.VrbZs8/_new 2021-03-03 18:36:05.235423305 +0100 @@ -1,7 +1,7 @@ # # spec file for package libhts # -# Copyright (c) 2020 SUSE LLC +# Copyright (c) 2021 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -17,9 +17,9 @@ Name: libhts -Version: 1.10.2 -%define sonum 3 +Version: 1.11 Release: 0 +%define sonum 3 Summary: C library for high-throughput sequencing data formats License: MIT Group: Productivity/Scientific/Other ++++++ htslib-1.10.2.tar.bz2 -> htslib-1.11.tar.bz2 ++++++ ++++ 14664 lines of diff (skipped)
