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File libhts.changes of Package libhts (Revision 88b5c3651f748f5515515bcd5919ab06)

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Fri Feb 19 01:11:53 UTC 2021 - Wang Jun <jgwang@suse.com>

- 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.

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Mon Feb 10 16:49:36 UTC 2020 - Todd R <toddrme2178@gmail.com>

- Include baselibs.conf as source file.
- Update baselibs.conf.

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Wed Feb  5 14:56:21 UTC 2020 - Todd R <toddrme2178@gmail.com>

- 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 README.large_positions.md for more information.
    * Added a SAM header API.
    * Major speed up to SAM reading and writing.  This also now supports
      multi-threading.
    * 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.

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Thu Sep  6 08:36:33 UTC 2018 - flyos@mailoo.org

- 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)

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Thu Jul 12 08:14:14 UTC 2018 - flyos@mailoo.org

- 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 
    Hickman).
  * 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.

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Wed Jul 12 09:34:35 UTC 2017 - flyos@mailoo.org

- Separated the binaries from the shared lib package

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Mon Jul 10 21:23:44 UTC 2017 - flyos@mailoo.org

- Cleaner structure of the spec file and baselibs.conf, 
  thanks to the amazing help of the packaging mailing list guys!

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Mon Jul 10 07:57:46 UTC 2017 - flyos@mailoo.org

- Update to 1.5
- Change in SONAME, updated the package name to libhts2
- New dependencies to libbz2 and lzma

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Sat Apr 30 16:39:18 UTC 2016 - flyos@mailoo.org

- Update to 1.3.1

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Sat Apr 30 16:25:54 UTC 2016 - flyos@mailoo.org

- Cleaner spec file
- Added baselibs.conf

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Thu Apr 21 15:57:58 UTC 2016 - flyos@mailoo.org

- Changed "./configure" and "make install" for "%configure" and 
  "%make_install"
- Moved "%_libdir/libhts.so" and "%_libdir/pkgconfig/htslib.pc" 
  to the *-devel package.

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Tue Apr 19 19:35:55 UTC 2016 - flyos@mailoo.org

- Initial release.

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File libhts.changes of Package libhts (Revision 88b5c3651f748f5515515bcd5919ab06)

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