Atri Bhattacharya
7815b6ea55
- 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
OBS-URL: https://build.opensuse.org/request/show/1137140
OBS-URL: https://build.opensuse.org/package/show/science/bedtools?expand=0&rev=7
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Fri Jan 5 18:30:02 UTC 2024 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to 2.31.1
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* Added new summary tool for basic sanity checks and quality
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control of interval files.
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* Added support for gzipp'ed FASTA files to getfasta and nuc.
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* Various typo and minor bug fixes
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-------------------------------------------------------------------
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Thu Sep 15 17:02:25 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to 2.30.0
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* Substantial improvements in the speed associated with parsing
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input files and in printing results.
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* Improved the stability and cleanliness of the code used for
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random number generation.
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* Cleaned up some lingering data type problems in the slop tool.
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* Added the -ignoreD option to the genomecov tool, which allows
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D CIGAR operations to be ignored when calculating coverage.
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* Added a fix for a bug that did not properly handle the
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splitting of intervals in BED12 records with one block.
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* Addressed numerical instability issues in the fisher tool.
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* Reference genomes can be read as an environment variable
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(CRAM_REFERENCE) when using CRAM input files.
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* Added a -rna option to the getfasta tool to allow support
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for RNA genomes.
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* Fixed input file format detection bugs arising in ZSH.
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* Clarifyed a confusing inconsistency in the documentation
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for the coverage tool.
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* Suppressed unnecessary warnings when reading GZIPP'ed files.
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* Fixed an overflow bug in the shuffle tool.
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* Fixed an data type bug in the shift tool.
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* Cleaned up the internal support for htslib.
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- Add missing lzma BuildRequires.
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- Removed obsolete rpmlintrc
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-------------------------------------------------------------------
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Tue Mar 31 07:55:27 UTC 2020 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to 2.29.2
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* Fixed a bug (#803) that mistakenly removed a BAM/CRAM header
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line (sorting criteria)
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- Update to 2.29.1
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* Fixed a bug that now allows blocked intersection to be counted
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based on unique base pairs of overlap. The resolution for issue
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750 in version 2.29.0 mistakenly allowed for fractional overlap
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to be counted based upon redundant overlap.
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* Moved to Github Continuous Integration for automatic testing.
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* Fixed a bug that injected erroneous quality values with BAM
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records had no valid quality values.
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* Fixed a bug that destroyed backwards compatibility in the
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getfasta tool. Thanks to Torsten Seeman for reporting this.
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* Fixed a corner case bug in the reldist tool.
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* Fixed a bug in the bedtobam tool that caused the last character
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in read names to be removed.
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* Fixed a bug causing a segfault in the jaccard tool.
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* Fixed a bug causing a corner case issue in the way coordinates
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are reported in the flank tool.
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- Update to 2.29.0
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* Changed LICENSE to MIT
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* Added a new -C option to the intersect tool that separately
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reports the count of intersections observed for each database
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(-b) file given. Formerly, the -c option reported to sum of
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all intersections observed across all database files.
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* Fixed an important bug in intersect that prevented some split
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reads from being counted properly with using the -split option
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with the -f option.
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* Fixed a bug in shuffle such that shuffled regions should have
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the same strand as the chose -incl region.
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* Added a new -L option to Limit the output of the `complement
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tool to solely the chromosomes that are represented in the
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-i file.
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* Fixed a regression in the multicov tool introduced in 2.28
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that caused incorrect counts.
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* Added support for multi-mapping reads in the bamtofastq tool.
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* Fixed a bug that prevented the “window” tool from properly
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adding interval “slop” to BAM records.
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* Fixed a bug that caused the slop tool to not truncate an
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interval’s end coordinate when it overlapped the end of a
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chromosome.
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* Added support for the “=” and “X” CIGAR operations to bamtobed.
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* Various other minor bug fixes and improvements to documentation.
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- Update to 2.28.0
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* Included support for htslib to enable CRAM support and
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long-term stability (Thanks to Hao Hou!)
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* Included support for genomes with large chromosomes by moving
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to 64-bit integers throughout the code base. Thanks to Brent
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Pedersen and John Marshall!
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* We now provide a statically-linked binary for LINUX (not OSX)
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systems (see "bedtools" link below).
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* As a result of the changes above, tools are ~10% faster.
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* Various minor bug fixes.
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-------------------------------------------------------------------
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Mon Oct 1 11:52:03 UTC 2018 - Bernhard Wiedemann <bwiedemann@suse.com>
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- Drop environment.pickle to make package build reproducible
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-------------------------------------------------------------------
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Thu Jul 12 10:55:48 UTC 2018 - flyos@mailoo.org
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- Cleaned spec file using spec-cleaner
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- Update to 2.27.1
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* Fixed a big memory leak and algorithmic flaw in the split option. Thanks to Neil Kindlon!
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* Resolved compilation errors on OSX High Sierra. Many thanks to @jonchang!
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* Fixed a bug in the shift tool that caused some intervals to exceed the end of the chromosome. Thanks to @wlholtz
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* Fixed major bug in groupby that prevented proper functionality.
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* Speed improvements to the shuffle tool.
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* Bug fixes to the p-value calculation in the fisher tool. Thanks to Brent Pedersen.
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* Allow BED headers to start with chrom or chr
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* Fixes to the "k-closest" functionality in the closest tool. Thanks to Neil Kindlon.
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* 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.
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* Many minor bug fixes and compilation improvements from Luke Goodsell.
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* Added the -fullHeader option to the maskfasta tool. Thanks to @ghuls.
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* Many bug fixes and performance improvements from John Marshall.
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* Fixed bug in the -N/-f behavior in subtract.
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* Full support for .fai files as genome (-g) files.
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* Many other minor bug fixes and functionality improvements.
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-------------------------------------------------------------------
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Fri Jan 20 09:16:14 UTC 2017 - badshah400@gmail.com
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- Clean up spec file:
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* Split out docs into a doc subpackage.
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* Remove unnecessary .buildinfo file from the rpm file list.
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* Remove exec bits from a file which is not supposed to be
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executable (not in an exec directory, and does not have
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a hashbang).
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* Remove EOL period from summary for %{name}-data package.
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- Add rpmlintrc file to suppress warnings about missing man pages,
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this is not something we can fix without upstream support.
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-------------------------------------------------------------------
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Fri Jan 20 00:31:33 UTC 2017 - flyos@mailoo.org
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- Initial build
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