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bedtools version 2.30.0

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@arq5x arq5x released this 23 Jan 20:10
· 86 commits to master since this release
  1. Thanks to Hao Hou (github: @38), we have made substantial improvements in the speed associated with parsing input files and in printing results. It turns our that these tasks consume a large proportion of run time, especially as input files increase in size. These changes result in a 2-3X improvement in speed, depending on input types, options, etc.
  2. Thanks to John Marshall (github: @jmarshall), who improved the stability and cleanliness of the code used for random number generation. These changes also squash a bug that arises on Debian systems.
  3. John Marshall cleaned up some lingering data type problems in the slop tool.
  4. Thanks to @gringer for adding the -ignoreD option to the genomecov tool, which allows D CIGAR operations to be ignored when calculating coverage. This is useful for long-read technologies with high INDEL error rates.
  5. Added a fix for a bug that did not properly handle the splitting of intervals in BED12 records with one block.
  6. Thanks to John Marshall (github: @jmarshall), we have addressed numerical instability issues in the fisher tool.
  7. Thanks to Hao Hou (github: @38), reference genomes can be read as an environment variable (CRAM_REFERENCE) when using CRAM input files.
  8. Added a -rna option to the getfasta tool to allow support for RNA genomes.
  9. Thanks to Hao Hou (github: @38), we fixed input file format detection bugs arising in ZSH.
  10. Thanks to Josh Shapiro (github:@jashapiro) for clarifying a confusing inconsistency in the documentation for the coverage tool.
  11. Thanks to Hao Hou (github: @38), we suppressed unnecessary warnings when reading GZIPP'ed files.
  12. Thanks to Hao Hou (github: @38), we fixed an overflow bug in the shuffle tool.
  13. Thanks to Hao Hou (github: @38), we fixed an data type bug in the shift tool.
  14. Thanks to John Marshall (github: @jmarshall) and Hao Hou (github: @38), we have cleaned up the internal support for htslib.