Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package libhts for openSUSE:Factory checked in at 2022-09-11 21:57:26 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/libhts (Old) and /work/SRC/openSUSE:Factory/.libhts.new.2083 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "libhts" Sun Sep 11 21:57:26 2022 rev:5 rq:1002325 version:1.16 Changes: -------- --- /work/SRC/openSUSE:Factory/libhts/libhts.changes 2022-05-04 15:11:00.076161005 +0200 +++ /work/SRC/openSUSE:Factory/.libhts.new.2083/libhts.changes 2022-09-11 21:57:27.357646086 +0200 @@ -1,0 +2,50 @@ +Thu Sep 8 21:40:07 UTC 2022 - Stefan Br??ns <[email protected]> + +- 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. + +------------------------------------------------------------------- Old: ---- htslib-1.15.1.tar.bz2 New: ---- htslib-1.16.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ libhts.spec ++++++ --- /var/tmp/diff_new_pack.4azelG/_old 2022-09-11 21:57:28.209648483 +0200 +++ /var/tmp/diff_new_pack.4azelG/_new 2022-09-11 21:57:28.213648495 +0200 @@ -16,8 +16,11 @@ # +# Upstream does not bump htscodecs SOVERSION on backwards incompatible changes +%define htscodecsminversion 1.3.0 + Name: libhts -Version: 1.15.1 +Version: 1.16 Release: 0 %define sonum 3 Summary: C library for high-throughput sequencing data formats @@ -27,7 +30,7 @@ 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: htscodecs-devel >= %{htscodecsminversion} BuildRequires: pkgconfig(bzip2) BuildRequires: pkgconfig(libcurl) BuildRequires: pkgconfig(liblzma) @@ -45,6 +48,7 @@ %package -n libhts%{sonum} Summary: C library for high-throughput sequencing data formats Group: System/Libraries +Requires: libhtscodecs2 >= %{htscodecsminversion} %description -n libhts%{sonum} HTSlib is an implementation of a unified C library for accessing common file formats, such as @@ -101,8 +105,6 @@ Summary: Header files and libraries for compiling against %{name} Group: Development/Libraries/C and C++ Requires: libhts%{sonum} = %{version} -Provides: libhts1-devel = %{version} -Obsoletes: libhts1-devel < 1.5 Requires: pkgconfig(bzip2) Requires: pkgconfig(libcurl) Requires: pkgconfig(liblzma) ++++++ htslib-1.15.1.tar.bz2 -> htslib-1.16.tar.bz2 ++++++ ++++ 31009 lines of diff (skipped)
