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Commits on Nov 24, 2014
Commits on Jul 5, 2013
  1. POD mistake

    bosborne committed Jul 5, 2013
Commits on Mar 16, 2013
Commits on Mar 12, 2013
  1. Bio::FeatureIO requires Config::Any, added that to Build.PL. Also fix…

    …ed miscellaneous POD warnings
    bosborne committed Mar 12, 2013
Commits on Feb 15, 2013
  1. adding test for ignore_seq_region method as well as a minor fix in Ge…

    …nericFeatureHandler to deal with undef directives (ie, to ignore them).
    scottcain committed Feb 15, 2013
  2. adding back in the ignore_ref_seq method; passes current tests, now h…

    …ave to add a test for the new method
    scottcain committed Feb 15, 2013
Commits on Feb 11, 2013
  1. Merge pull request #1 from carandraug/master

    merge changes from bioperl-live
    cjfields committed Feb 11, 2013
Commits on Feb 10, 2013
  1. Preferring get_all_tags() and get_tag_values() over all_tags() and ea…

    …ch_tag_value() in SeqFeatures for consistency + compliance with SeqFeatureI + indentation cleaning
    fangly committed with carandraug Mar 23, 2012
  2. SeqFeature::Annotated tests

    fangly committed with carandraug Mar 5, 2012
  3. More informative error message

    fangly committed with carandraug Oct 10, 2011
  4. Initialize Bio::SeqIO object throught the seqio() method instead of n…

    …ext_read() and not no initialize Bio::SeqIO before we have reached the ##FASTA section of the GFF stream
    fangly committed with carandraug Oct 10, 2011
  5. POD clarifications

    fangly committed with carandraug Oct 10, 2011
  6. POD update

    fangly committed with carandraug Sep 5, 2011
  7. fix spelling errors, fixes #3228

    Chris Fields committed with carandraug May 10, 2011
  8. A few things going on here:

      for Bio::DB::GFF and the gff loading scripts, added a warning message if the
      user is loading gff3.
    
      for Bio::FeatureIO::gff, it's test and the knownGene.gff3 sample data, there
      is a fix to NOT unescape URI codes in the Target values, per the GFF3 spec.
    scottcain committed with carandraug Apr 1, 2011
  9. tiny change to Bio::FeatureIO::gff to allow the gmod chado gff3 bulk …

    …loader
    
    to not choke when the gff file has ##sequence-region directives.  The loader
    is documented not to support this, but now it will quitely ignore those
    directives.
    scottcain committed with carandraug Aug 11, 2010
  10. fixed wrong interpretation of locations in bed files; added a test fi…

    …le plus tests for this
    pkensche committed with carandraug May 14, 2010
  11. speling

    svn path=/bioperl-live/trunk/; revision=16917
    cjfields committed with carandraug Mar 11, 2010
  12. remove 'officially sanctioned' hoo rah from module, replace it with a…

    … warning indicating it's current state
    
    svn path=/bioperl-live/trunk/; revision=16916
    cjfields committed with carandraug Mar 11, 2010
  13. silence warning (uninit value)

    svn path=/bioperl-live/trunk/; revision=16854
    cjfields committed with carandraug Feb 19, 2010
  14. using the _pushback method instead of seek per Jason's suggestion.

    svn path=/bioperl-live/trunk/; revision=16468
    scain committed with carandraug Dec 16, 2009
  15. Fixing a bug that caused the first sequence in a ##FASTA section to b…

    …e lost; the problem was that Bio::SeqIO::fasta sets \n> as the line separator, but during processing, Bio::FeatureIO::gff swallowed the \n before sending the filehandle to SeqIO. Now when fasta_mode is set, it rewinds the filehandle to get the preceeding line's \n.
    
    svn path=/bioperl-live/trunk/; revision=16465
    scain committed with carandraug Dec 16, 2009
  16. [bug 2843]

    * check phase value prior to calling its value (Cass Johnston)
    
    svn path=/bioperl-live/trunk/; revision=16270
    cjfields committed with carandraug Oct 25, 2009
  17. [cage cleaning]

    * fixing POD links and errors
    
    svn path=/bioperl-live/trunk/; revision=16110
    cjfields committed with carandraug Sep 16, 2009
  18. [cage cleaning]

    * the POD parser doesn't like whitespace in paragraphs
    * can't use L<> with emails
    
    svn path=/bioperl-live/trunk/; revision=16108
    cjfields committed with carandraug Sep 16, 2009
  19. adding pod FEEDBACK:Support section, with associated bioperl.lisp

    template mods
    
    svn path=/bioperl-live/trunk/; revision=15549
    maj committed with carandraug Feb 21, 2009