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htsfile-1.10.2-lp152.2.4.1 RPM for aarch64

From OpenSuSE Ports Leap 15.2 updates for aarch64

Name: htsfile Distribution: openSUSE Leap 15.2
Version: 1.10.2 Vendor: openSUSE
Release: lp152.2.4.1 Build date: Mon Aug 16 15:28:38 2021
Group: Productivity/Scientific/Other Build host: obs-arm-8
Size: 712615 Source RPM: libhts-1.10.2-lp152.2.4.1.src.rpm
Summary: Identify high-throughput sequencing data files from the HTSlib project
HTSlib is an implementation of a unified C library for accessing common file formats, such as
SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by
samtools and bcftools.
HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index).
The HTSlib file reader first looks for the new index and then for the old if the new index is absent.
This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and
the bgzip compression utility.






* Thu Aug 05 2021 Pierre Bonamy <>
  - CVE-2020-36403.diff: Add patch fixing CVE-2020-36403 #boo1187917
* Mon Feb 10 2020 Todd R <>
  - Include baselibs.conf as source file.
  - Update baselibs.conf.
* Wed Feb 05 2020 Todd R <>
  - Update to release 1.10.2
    * This is a release fix that corrects minor inconsistencies discovered in
      previous deliverables.
  - Update to release 1.10.1
    * The support for 64-bit coordinates in VCF brought problems for files
      not conforming to VCF/BCF specification. While previous versions would
      make out-of-range values silently overflow creating nonsense values
      but parseable file, the version 1.10 would silently create an invalid BCF.
  - Update to release 1.10
    + Brief summary
    * Addition of support for references longer than 2Gb (NB: SAM and VCF
      formats only, not their binary counterparts).  This may need changes
      in code using HTSlib.  See for more information.
    * Added a SAM header API.
    * Major speed up to SAM reading and writing.  This also now supports
    * We can now auto-index on-the-fly while writing a file.  This also
      includes to bgzipped SAM.gz.
    * Overhaul of the S3 interface, which now supports version 4
      signatures.  This also makes writing to S3 work.
* Thu Sep 06 2018
  - Update to 1.9
    * If `./configure` fails, `make` will stop working until either configure
      is re-run successfully, or `make distclean` is used.  This makes
      configuration failures more obvious.  (#711, thanks to John Marshall)
    * The default SAM version has been changed to 1.6.  This is in line with the
      latest version specification and indicates that HTSlib supports the
      CG tag used to store long CIGAR data in BAM format.
    * bgzip integrity check option '--test' (#682, thanks to @sd4B75bJ, @jrayner)
    * Faidx can now index fastq files as well as fasta.  The fastq index adds
      an extra column to the `.fai` index which gives the offset to the quality
      values.  New interfaces have been added to `htslib/faidx.h` to read the
      fastq index and retrieve the quality values.  It is possible to open
      a fastq index as if fasta (only sequences will be returned), but not
      the other way round. (#701)
    * New API interfaces to add or update integer, float and array aux tags. (#694)
    * Add `level=<number>` option to `hts_set_opt()` to allow the compression
      level to be set.  Setting `level=0` enables uncompressed output. (#715)
    * Improved bgzip error reporting.
    * Better error reporting when CRAM reference files can't be opened. (#706)
    * Fixes to make tests work properly on Windows/MinGW - mainly to handle
      line ending differences. (#716)
    * Efficiency improvements:
    - Small speed-up for CRAM indexing.
    - Reduce the number of unnecessary wake-ups in the thread pool. (#703)
    - Avoid some memory copies when writing data, notably for uncompressed
      BGZF output. (#703)
    * Bug fixes:
    - Fix multi-region iterator bugs on CRAM files. (#684)
    - Fixed multi-region iterator bug that caused some reads to be skipped
      incorrectly when reading BAM files. (#687)
    - Fixed synced_bcf_reader() bug when reading contigs multiple times. (#691,
      reported by @freeseek)
    - Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary
      when removing samples. (#692, reported by @freeseek)
    - Fixed bug where the VCF record ref length was calculated incorrectly
      if an INFO END tag was present. (71b00a)
    - Fixed warnings found when compiling with gcc 8.1.0. (#700)
    - sam_hdr_read() and sam_hdr_write() will now return an error code
      if passed a NULL file pointer, instead of crashing.
    - Fixed possible negative array look-up in sam_parse1() that somehow
      escaped previous fuzz testing. (#731, reported by @fCorleone)
    - Fixed bug where cram range queries could incorrectly report an error
      when using multiple threads. (#734, reported by Brent Pedersen)
    - Fixed very rare rANS normalisation bug that could cause an assertion
      failure when writing CRAM files. (#739, reported by @carsonhh)
* Thu Jul 12 2018
  - Better formatting of the descriptions
  - Spec file cleaned up using spec-cleaner
  - Update to 1.8
    * The URL to get sequences from the EBI reference server has been changed
      to https://.  This is because the EBI no longer serve sequences via
      plain HTTP - requests to the http:// endpoint just get redirected.
      HTSlib needs to be linked against libcurl to download https:// URLs,
      so CRAM users who want to get references from the EBI will need to
      run configure and ensure libcurl support is enabled using the
    - -enable-libcurl option.
    * Added libdeflate as a build option for alternative faster compression and
      decompression.  Results vary by CPU but compression should be twice as fast
      and decompression faster.
    * It is now possible to set the compression level in bgzip.  (#675; thanks
      to Nathan Weeks).
    * bgzip now gets its own manual page.
    * CRAM encoding now stored MD and NM tags verbatim where the reference
      contains 'N' characters, to work around ambiguities in the SAM
      specification (samtools #717/762).
      Also added "store_md" and "store_nm" cram-options for forcing these
      tags to be stored at all locations.  This is best when combined with
      a subsequent decode_md=0 option while reading CRAM.
    * Multiple CRAM bug fixes, including a fix to free and the subsequent reuse of
      references with `-T ref.fa`. (#654; reported by Chris Saunders)
    * CRAM multi-threading bugs fixed: don't try to call flush on reading;
      processing of multiple range queries; problems with multi-slice containers.
    * Fixed crashes caused when decoding some cramtools produced CRAM files.
    * Fixed a couple of minor rANS issues with handling invalid data.
    * Fixed bug where probaln_glocal() tried to allocate far more memory than
      needed when the query sequence was much longer than the reference.  This
      caused crashes in samtools and bcftools mpileup when used on data with very
      long reads. (#572, problem reported by Felix Bemm via minimap2).
    * sam_prop_realn() now returns -1 (the same value as for unmapped reads)
      on reads that do not include at least one 'M', 'X' or '=' CIGAR operator,
      and no longer adds BQ or ZQ tags.  BAQ adjustments are only made to bases
      covered by these operators so there is no point in trying to align
      reads that do not have them. (#572)
    * BAM: HTSlib now supports BAMs which include CIGARs with more than
      65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8).
    * BCF/VCF:
    - Removed the need for long double in pileup calculations.
    - Sped up the synced reader in some situations.
    - Bug fixing: removed memory leak in bcf_copy.
    * CRAM:
    - Added support for HTS_IDX_START in cram iterators.
    - Easier to build when lzma header files are absent.
    - Bug fixing: a region query with REQUIRED_FIELDS option to
      disable sequence retrieval now gives correct results.
    - Bug fixing: stop queries to regions starting after the last
      read on a chromosome from incorrectly reporting errors
      (#651, #653; reported by Imran Haque and @egafni via pysam).
    * Multi-region iterator: The new structure takes a list of regions and
      iterates over all, deduplicating reads in the process, and producing a
      full list of file offset intervals. This is usually much faster than
      repeatedly using the old single-region iterator on a series of regions.
    * Curl improvements:
    - Add Bearer token support via HTS_AUTH_LOCATION env (#600).
    - Use CURL_CA_BUNDLE environment variable to override the CA (#622;
      thanks to Garret Kelly & David Alexander).
    - Speed up (removal of excessive waiting) for both http(s) and ftp.
    - Avoid repeatedly reconnecting by removal of unnecessary seeks.
    - Bug fixing: double free when libcurl_open fails.
    * BGZF block caching, if enabled, now performs far better (#629; reported
      by Ram Yalamanchili).
    * Added an hFILE layer for in-memory I/O buffers (#590; thanks to Thomas
    * Tidied up the drand48 support (intended for systems that do not
      provide this function).
    * Fixed bug where iterators on CRAM files did not propagate error return
      values to the caller correctly.  Thanks go to Chris Saunders.
    * Overhauled Windows builds.  Building with msys2/mingw64 now works
      correctly and passes all tests.
    * More improvements to logging output (thanks again to Anders Kaplan).
    * Return codes from sam_read1() when reading cram have been made
      consistent with those returned when reading sam/bam.  Thanks to
      Chris Saunders (#575).
    * BGZF CRC32 checksums are now always verified.
    * It's now possible to set nthreads = 1 for cram files.
    * hfile_libcurl has been modified to make it thread-safe.  It's also
      better at handling web servers that do not honour byte range requests
      when attempting to seek - it now sets errno to ESPIPE and keeps
      the existing connection open so callers can revert to streaming mode
      it they want to.
    * hfile_s3 now recalculates access tokens if they have become stale.  This
      fixes a reported problem where authentication failed after a file
      had been in use for more than 15 minutes.
    * Fixed bug where remote index fetches would fail to notice errors when
      writing files.
    * bam_read1() now checks that the query sequence length derived from the
      CIGAR alignment matches the sequence length in the BAM record.
* Wed Jul 12 2017
  - Separated the binaries from the shared lib package
* Mon Jul 10 2017
  - Cleaner structure of the spec file and baselibs.conf,
    thanks to the amazing help of the packaging mailing list guys!
* Mon Jul 10 2017
  - Update to 1.5
  - Change in SONAME, updated the package name to libhts2
  - New dependencies to libbz2 and lzma
* Sat Apr 30 2016
  - Update to 1.3.1
* Sat Apr 30 2016
  - Cleaner spec file
  - Added baselibs.conf
* Thu Apr 21 2016
  - Changed "./configure" and "make install" for "%configure" and
  - Moved "%_libdir/" and "%_libdir/pkgconfig/htslib.pc"
    to the *-devel package.
* Tue Apr 19 2016
  - Initial release.



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Fabrice Bellet, Mon Nov 29 23:59:34 2021