Permalink
Commits on May 10, 2013
  1. remove useless cruft, add note

    Chris Fields committed May 10, 2013
Commits on Mar 12, 2013
  1. Bio::FeatureIO requires Config::Any, added that to Build.PL. Also fix…

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

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

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

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

    fangly committed with carandraug Mar 23, 2012
    …ch_tag_value() in SeqFeatures for consistency + compliance with SeqFeatureI + indentation cleaning
  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…

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

    scottcain committed with carandraug Apr 1, 2011
      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.
  9. tiny change to Bio::FeatureIO::gff to allow the gmod chado gff3 bulk …

    scottcain committed with carandraug Aug 11, 2010
    …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.
  10. fixed wrong interpretation of locations in bed files; added a test fi…

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

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

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

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

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

    scain committed with carandraug Dec 16, 2009
    …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
  16. [bug 2843]

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

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

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

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

    cjfields committed with carandraug Dec 23, 2008
    svn path=/bioperl-live/trunk/; revision=15238
  21. small typo

    cjfields committed with carandraug Dec 21, 2008
    svn path=/bioperl-live/trunk/; revision=15224