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Bio-ToolBox-v2.02

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@tjparnell tjparnell released this 05 Aug 19:24
· 61 commits to master since this release
  • Add support for newer versions of UCSC utilities that no longer
    allow reading from standard input, particularly wigToBigWig.
    Temporary wig files are written first and then the utility is
    called. Updates made to bam2wig.pl, data2wig.pl, and manipulate_wig.pl.
  • Add public headers() boolean method for Data objects.
  • Changed duplicate() method for Stream objects to allow generating
    a duplicate Data object if no output file name is provided.
  • Various library bug fixes and improvements, including reading bedGraph
    files, writing simple text files, handling spaces in numeric index lists,
    automatic checking of extensions, parsing annotation files into tables,
    and speeding up row deletion in large data tables.
  • Fix issues with default output filenames in data collection scripts
    get_datasets.pl, get_binned_data.pl, and get_relative_data.pl. Default is
    to reuse input filename unless it was parsed, in which case the basename
    plus txt is used. Also fix bugs regarding mismatched column names when
    explicitly not parsing input annotation files.
  • Fix bug with leaving behind MergeDatasetCoordinate column in merge_datasets.pl.
  • Fix bug with using new column name instead of original column name in
    message statements when manipulating columns in manipulate_datasets.pl.
  • Fix possible bug with undefined strand when automatically flipping coordinates
    of reversed intervals in SeqFeature objects.
  • Remove deprecated and unused functions.
  • Add missing POD method sections for complete coverage.