Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package libhts for openSUSE:Factory checked in at 2022-05-04 15:10:42 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/libhts (Old) and /work/SRC/openSUSE:Factory/.libhts.new.1538 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "libhts" Wed May 4 15:10:42 2022 rev:4 rq:974395 version:1.15.1 Changes: -------- --- /work/SRC/openSUSE:Factory/libhts/libhts.changes 2021-05-18 18:27:13.318759694 +0200 +++ /work/SRC/openSUSE:Factory/.libhts.new.1538/libhts.changes 2022-05-04 15:11:00.076161005 +0200 @@ -1,0 +2,76 @@ +Wed Apr 20 19:32:52 UTC 2022 - Ferdinand Thiessen <r...@fthiessen.de> + +- Use system provided libhtscodecs +- Update to version 1.15.1 + * Security fix: Fixed broken error reporting in the sam_cap_mapq() + function, due to a missing hts_log() parameter. + Prior to this fix it was possible to abuse the log message format + string by passing a specially crafted alignment record to + this function. + * Fixed excessive memory used by multi-threaded SAM output on long + reads. + * Fixed a bug where tabix would misinterpret region specifiers + starting at position 0. + * The VCF header parser will now issue a warning if it finds an + INFO header with Type=Flag but Number not equal to 0. +- Update to version 1.15 + * Bgzip now has a --keep option to not remove the input file + after compressing. + * Improved file format detection so some BED files are no longer + detected as FASTQ or FASTA. + * Added xz (lzma), zstd and D4 formats to the file type detection + functions. We don't actively support reading these data types, + but function calls and htsfile can detect them. + * CRAM now also uses libdeflate for read-names if the libdeflate + version is new enough (1.9 onwards). Previously we used zlib for + this due to poor performance of libdeflate. + * The VCF and BCF readers will now issue a warning if contig, + INFO or FORMAT IDs do not match the formats described in the + VCFv4.3 specification. + * Bug fixes +- Update to version 1.14 + * Added a keep option to bgzip to leave the original file untouched. + * endpos has been added to the filter language, giving the position + of the rightmost mapped base as measured by the CIGAR string. + * Interfaces have been added to interpret the new base modification + tags added to the SAMtags document in samtools/hts-specs#418. + * New API functions hts_flush()/sam_flush()/bcf_flush() for + flushing output htsFile/samFile/vcfFile streams. + * The synced_bcf_reader now sorts lines with symbolic alleles by + END tag as well as POS. + * Added synced_bcf_reader options BCF_SR_REGIONS_OVERLAP and + BCF_SR_TARGETS_OVERLAP for better control of records that start + outside the desired region but overlap it are handled. + * HTSlib will now accept long-cigar CG:B: tags made by htsjdk which + don't quite follow the specification properly + * The FASTA and FASTQ readers get an option to skip over the first + item on the header line, and use the second as the read name. + * HTSlib is now more strict when parsing the VCF samples line + * HTSlib will now warn if it looks like the header has been + corrupted by diagnostic messages from the program that made it. + * File format detection will now recognise signatures for + XZ, Zstd and D4 files (note that HTSlib will not read them yet). + * Bug fixes +- Update to version 1.13 + * In case a PG header line has multiple ID tags supplied by other + applications, the header API now selects the first one encountered + as the identifying tag and issues a warning when detecting + subsequent ID tags. + * VCF header reading function (vcf_hdr_read) no longer tries to + download a remote index file by default. + * Support reading and writing FASTQ format in the same way as SAM, + BAM or CRAM. Records read from a FASTQ file will be treated as + unmapped data. + * Added GCP requester pays bucket access. + * Made mpileup's overlap removal choose which copy to remove at + random instead of always removing the second one. + * It is now possible to use platform specific BAQ parameters. + * A new hts_bin_level API function has been added, to compute the + level of a given bin in the binning index. + * Related to the above, a new API method, hts_idx_nseq, + now returns the total number of contigs from an index. + * Added bracket handling to bcf_hdr_parse_line, + for use with ##META lines. + * Bug fixes + +------------------------------------------------------------------- Old: ---- htslib-1.12.tar.bz2 New: ---- htslib-1.15.1.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ libhts.spec ++++++ --- /var/tmp/diff_new_pack.XCkVhr/_old 2022-05-04 15:11:00.676161743 +0200 +++ /var/tmp/diff_new_pack.XCkVhr/_new 2022-05-04 15:11:00.684161753 +0200 @@ -1,7 +1,7 @@ # # spec file for package libhts # -# Copyright (c) 2021 SUSE LLC +# Copyright (c) 2022 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -17,7 +17,7 @@ Name: libhts -Version: 1.12 +Version: 1.15.1 Release: 0 %define sonum 3 Summary: C library for high-throughput sequencing data formats @@ -27,6 +27,7 @@ Source0: https://github.com/samtools/htslib/releases/download/%{version}/htslib-%{version}.tar.bz2 Source100: baselibs.conf BuildRequires: gcc-c++ +BuildRequires: htscodecs-devel >= 1.2.2 BuildRequires: pkgconfig(bzip2) BuildRequires: pkgconfig(libcurl) BuildRequires: pkgconfig(liblzma) @@ -114,12 +115,15 @@ %setup -q -n htslib-%{version} %build -%configure -make %{?_smp_mflags} +%configure --with-external-htscodecs --disable-static +%make_build %install %make_install +# remove static library rm %{buildroot}%{_libdir}/libhts.a +# fix permissions +chmod 0755 %{buildroot}%{_libdir}/libhts.so.* %post -n libhts%{sonum} -p /sbin/ldconfig %postun -n libhts%{sonum} -p /sbin/ldconfig @@ -146,8 +150,7 @@ %{_mandir}/man7/* %files devel -%{_includedir}/htslib/. -%{_includedir}/htslib/*.h +%{_includedir}/htslib %{_libdir}/libhts.so %{_libdir}/pkgconfig/htslib.pc ++++++ htslib-1.12.tar.bz2 -> htslib-1.15.1.tar.bz2 ++++++ ++++ 10248 lines of diff (skipped)
