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BioToolBox-v1.69

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@tjparnell tjparnell released this 24 Sep 02:19
· 194 commits to master since this release
  • Revise genomic sorting by introducing a sane, logical chromosome
    ordering that smartly handles numerical, Roman, contigs, and
    alternate names. Sorting is done by both start and end coordinates.
    Sorting speed modestly improved.
  • Improve handling of coordinates of Data Feature objects, including
    caching and setting.
  • Add support for narrowPeak summit coordinate as reference point
    in multiple scripts.
  • Improve handling of databases, including bigWigSet feature types.
    Make simplification of dataset names a little less aggressive.
  • Include options for excluding chromosomes and/or intervals when
    generating a new list of genomic bins
  • Improve tasting of file formats, keeping the file format of parsed files
    in the Data object.
  • Allow non-stranded values when parsing UCSC files, including bed files.
  • Optimize scoring subroutines
  • Remove legacy subroutines from utility module
  • Include new test file for utility functions
  • Numerous other small changes and fixes