File bedtools.changes of Package bedtools

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File bedtools.changes of Package bedtools

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Fri Jan  5 18:30:02 UTC 2024 - Stefan Brüns <stefan.bruens@rwth-aachen.de>

- Update to 2.31.1
  * Added new summary tool for basic sanity checks and quality
    control of interval files.
  * Added support for gzipp'ed FASTA files to getfasta and nuc.
  * Various typo and minor bug fixes

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Thu Sep 15 17:02:25 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>

- Update to 2.30.0
  * Substantial improvements in the speed associated with parsing
    input files and in printing results.
  * Improved the stability and cleanliness of the code used for
    random number generation.
  * Cleaned up some lingering data type problems in the slop tool.
  * Added the -ignoreD option to the genomecov tool, which allows
    D CIGAR operations to be ignored when calculating coverage.
  * Added a fix for a bug that did not properly handle the
    splitting of intervals in BED12 records with one block.
  * Addressed numerical instability issues in the fisher tool.
  * Reference genomes can be read as an environment variable
    (CRAM_REFERENCE) when using CRAM input files.
  * Added a -rna option to the getfasta tool to allow support
    for RNA genomes.
  * Fixed input file format detection bugs arising in ZSH.
  * Clarifyed a confusing inconsistency in the documentation
    for the coverage tool.
  * Suppressed unnecessary warnings when reading GZIPP'ed files.
  * Fixed an overflow bug in the shuffle tool.
  * Fixed an data type bug in the shift tool.
  * Cleaned up the internal support for htslib.
- Add missing lzma BuildRequires.
- Removed obsolete rpmlintrc

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Tue Mar 31 07:55:27 UTC 2020 - Stefan Brüns <stefan.bruens@rwth-aachen.de>

- Update to 2.29.2
  * Fixed a bug (#803) that mistakenly removed a BAM/CRAM header
    line (sorting criteria)
- Update to 2.29.1
  * Fixed a bug that now allows blocked intersection to be counted
    based on unique base pairs of overlap. The resolution for issue
    750 in version 2.29.0 mistakenly allowed for fractional overlap
    to be counted based upon redundant overlap.
  * Moved to Github Continuous Integration for automatic testing.
  * Fixed a bug that injected erroneous quality values with BAM
    records had no valid quality values.
  * Fixed a bug that destroyed backwards compatibility in the
    getfasta tool. Thanks to Torsten Seeman for reporting this.
  * Fixed a corner case bug in the reldist tool.
  * Fixed a bug in the bedtobam tool that caused the last character
    in read names to be removed.
  * Fixed a bug causing a segfault in the jaccard tool.
  * Fixed a bug causing a corner case issue in the way coordinates
    are reported in the flank tool.
- Update to 2.29.0
  * Changed LICENSE to MIT
  * Added a new -C option to the intersect tool that separately
    reports the count of intersections observed for each database
    (-b) file given. Formerly, the -c option reported to sum of
    all intersections observed across all database files.
  * Fixed an important bug in intersect that prevented some split
    reads from being counted properly with using the -split option
    with the -f option.
  * Fixed a bug in shuffle such that shuffled regions should have
    the same strand as the chose -incl region.
  * Added a new -L option to Limit the output of the `complement
    tool to solely the chromosomes that are represented in the
    -i file.
  * Fixed a regression in the multicov tool introduced in 2.28
    that caused incorrect counts.
  * Added support for multi-mapping reads in the bamtofastq tool.
  * Fixed a bug that prevented the “window” tool from properly
    adding interval “slop” to BAM records.
  * Fixed a bug that caused the slop tool to not truncate an
    interval’s end coordinate when it overlapped the end of a
    chromosome.
  * Added support for the “=” and “X” CIGAR operations to bamtobed.
  * Various other minor bug fixes and improvements to documentation.
- Update to 2.28.0
  * Included support for htslib to enable CRAM support and
    long-term stability (Thanks to Hao Hou!)
  * Included support for genomes with large chromosomes by moving
    to 64-bit integers throughout the code base. Thanks to Brent
    Pedersen and John Marshall!
  * We now provide a statically-linked binary for LINUX (not OSX)
    systems (see "bedtools" link below).
  * As a result of the changes above, tools are ~10% faster.
  * Various minor bug fixes.

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Mon Oct  1 11:52:03 UTC 2018 - Bernhard Wiedemann <bwiedemann@suse.com>

- Drop environment.pickle to make package build reproducible

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Thu Jul 12 10:55:48 UTC 2018 - flyos@mailoo.org

- Cleaned spec file using spec-cleaner
- Update to 2.27.1
    * Fixed a big memory leak and algorithmic flaw in the split option. Thanks to Neil Kindlon!
    * Resolved compilation errors on OSX High Sierra. Many thanks to @jonchang!
    * Fixed a bug in the shift tool that caused some intervals to exceed the end of the chromosome. Thanks to @wlholtz
    * Fixed major bug in groupby that prevented proper functionality.
    * Speed improvements to the shuffle tool.
    * Bug fixes to the p-value calculation in the fisher tool. Thanks to Brent Pedersen.
    * Allow BED headers to start with chrom or chr
    * Fixes to the "k-closest" functionality in the closest tool. Thanks to Neil Kindlon.
    * Fixes to the output of the freqasc, freqdesc, distinct_sort_num and distinct_sort, and num_desc operations in the groupby tool. Thanks to @ghuls.
    * Many minor bug fixes and compilation improvements from Luke Goodsell.
    * Added the -fullHeader option to the maskfasta tool. Thanks to @ghuls.
    * Many bug fixes and performance improvements from John Marshall.
    * Fixed bug in the -N/-f behavior in subtract.
    * Full support for .fai files as genome (-g) files.
    * Many other minor bug fixes and functionality improvements.

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Fri Jan 20 09:16:14 UTC 2017 - badshah400@gmail.com

- Clean up spec file:
  * Split out docs into a doc subpackage.
  * Remove unnecessary .buildinfo file from the rpm file list.
  * Remove exec bits from a file which is not supposed to be
    executable (not in an exec directory, and does not have
    a hashbang).
  * Remove EOL period from summary for %{name}-data package.
- Add rpmlintrc file to suppress warnings about missing man pages,
  this is not something we can fix without upstream support.

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Fri Jan 20 00:31:33 UTC 2017 - flyos@mailoo.org

- Initial build

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