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Commits on Jan 9, 2015
  1. @carandraug
Commits on Mar 29, 2014
  1. @cjfields
Commits on Jan 16, 2014
  1. @fjossandon

    gff.pm: Optimized the Windows ending bug fix by moving the code

    fjossandon authored
    from "next_dataset" to "_initialize", so is only run once per
    file and then buffered on $self. The $self->{termination_length}
    stores the calculated length of the line ending characters.
    Since now the value is buffered, I removed the line endings just
    after _readline, so the multiple chomps are not needed.
Commits on Dec 6, 2013
  1. @fjossandon

    Bio::FeatureIO::gff.pm: Using bare equality without explicit variable

    fjossandon authored
    in "directive" caused a bug where "$directive = '#'" matched
    "elsif ('genome-build') {", instead of the proper conditional.
    Adding explicit "$_ eq" in the conditionals fixed it.
  2. @fjossandon

    Bio::FeatureIO::gff.pm: Windows compatibility fix, added a correction

    fjossandon authored
    to byte positions for ghost '\r'.
  3. @fjossandon
Commits on Nov 29, 2013
  1. @cmungall

    Removed cruft. Added docs

    cmungall authored
Commits on Jul 11, 2013
  1. @cmungall
  2. @cmungall
  3. @cmungall

    strands

    cmungall authored
  4. @cmungall

    initial pass at faldo writer

    cmungall authored
Commits on Jul 9, 2013
  1. simpify

    Chris Fields authored
  2. fix stoopid thinko on attributes

    Chris Fields authored
Commits on May 10, 2013
  1. no need to set these every time, make them state vars

    Chris Fields authored
  2. clean up a major bottleneck with feature generation

    Chris Fields authored
  3. move POD to end

    Chris Fields authored
  4. fix topicalizer bug

    Chris Fields authored
  5. remove useless cruft, add note

    Chris Fields authored
Commits on Mar 12, 2013
  1. @bosborne

    Bio::FeatureIO requires Config::Any, added that to Build.PL. Also fix…

    bosborne authored
    …ed miscellaneous POD warnings
Commits on Feb 15, 2013
  1. @scottcain

    adding test for ignore_seq_region method as well as a minor fix in Ge…

    scottcain authored
    …nericFeatureHandler to deal with undef directives (ie, to ignore them).
  2. @scottcain

    adding back in the ignore_ref_seq method; passes current tests, now h…

    scottcain authored
    …ave to add a test for the new method
Commits on Feb 10, 2013
  1. @carandraug
  2. @carandraug
Commits on Apr 13, 2012
  1. flip logic

    Chris Fields authored
  2. use for() instead of given()

    Chris Fields authored
Commits on Dec 7, 2011
  1. @rbuels
  2. @rbuels

    clean up some unused code

    rbuels authored
Commits on Oct 11, 2011
  1. @fangly

    POD clarifications

    fangly authored
  2. @fangly

    More informative error message

    fangly authored
Commits on Mar 14, 2011
  1. @rbuels
  2. @rbuels
Commits on Mar 8, 2011
  1. @rbuels

    implement GFF3 writing

    rbuels authored
  2. @rbuels
  3. <headsmack>unescape, not escape</headsmack>

    Chris Fields authored
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