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branch: topic/bug-2701
Commits on Apr 6, 2011
  1. fix conflicts with origin topic branch

    Chris Fields authored
    Merge remote branch 'origin/topic/bug-2701' into topic/bug-2701
    
    Conflicts:
    	Bio/AlignIO/mummer.pm
    	t/AlignIO/mummer.t
  2. get basic tests running and clean up code

    Chris Fields authored
  3. get basic tests running and clean up code

    Chris Fields authored
  4. @genehack

    move Bio::AlignIO::mummer to proper location

    genehack authored Chris Fields committed
    pointed out by Dan Kortschak in email -- thanks again Dan.
  5. @genehack

    Bio::Align::mummer module

    genehack authored Chris Fields committed
    includes minimal, non-BioPerl-compliant tests in t/AlignIO/mummer.t
    Tests need to be BioPerl-ized and greatly expanded.
    Related to http://bugzilla.open-bio.org/show_bug.cgi?id=2701
  6. @genehack

    Bio::Seq::RelocatableSeq module

    genehack authored Chris Fields committed
    This is required for supporting Bio::Align::mummer.
    Tests forthcoming.
    Related to http://bugzilla.open-bio.org/show_bug.cgi?id=2701
  7. Allow falling back to any strigified Bio::AnnotationI for 'gene_name'

    Chris Fields authored
    (along with tests), fixes #3153.
  8. * add tests that check trucated sequence length matches the qual data

    Chris Fields authored
    length, fixes #2891
    * note that the raw FASTQ string is NOT stored in the instances
  9. * 'use vars' -> our

    Chris Fields authored
    * run-time modification of @ISA is extremely evil and points to a problem
    that should be fixed in other ways.  Commenting this out still passes
    tests; I openly implore anyone who used such evilness to please find
    a better fix
Commits on Apr 5, 2011
  1. @rbuels

    add maintenance/find_mod_deps.pl, which lists (non-core) dependencies…

    rbuels authored
    … of the whole distribution, or just the set of files and dirs specified at the command line
  2. moved functions to Bio::SearchIO so they can be used generically, tho…

    Chris Fields authored
    …ugh completely untested, refs #2247
Commits on Apr 4, 2011
  1. rework to optimize a bit, again for bug #3172

    Chris Fields authored
  2. Revert "test hook again (anyone getting annoyed by this yet?)"

    Chris Fields authored
    This reverts commit d74316b.
    and also fixes #3189
  3. test hook again (anyone getting annoyed by this yet?)

    Chris Fields authored
  4. test hook

    Chris Fields authored
  5. test hook

    Chris Fields authored
  6. test hook, fingers crossed

    Chris Fields authored
  7. add patch that fixes #3190, courtesy Ali Walsh

    Chris Fields authored
Commits on Apr 2, 2011
  1. @lstein

    fixed bug in coverage statistics calculations that prevented correct …

    lstein authored
    …accumulation of coverage counts when multiple feature types requested
Commits on Apr 1, 2011
  1. @lstein
  2. @scottcain

    A few things going on here:

    scottcain authored
      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.
Commits on Mar 31, 2011
  1. test hook again

    Chris Fields authored
  2. test hook again

    Chris Fields authored
  3. @DaveMessina
  4. test post-receive again

    Chris Fields authored
  5. @DaveMessina
Commits on Mar 30, 2011
  1. @DaveMessina

    Merge commit 'b8cd8ed'

    DaveMessina authored
  2. @DaveMessina

    Merge commit '8905527'

    DaveMessina authored
  3. GuessSeqFormat tests - build it and they will come.

    kortschak authored
  4. Add VCF guesser. Example vcf format for testing - provided from http:…

    kortschak authored
    …//www.1000genomes.org/wiki/analysis/vcf4.0 with modification according to definition (spaces -> \t).
Commits on Mar 29, 2011
  1. retest hook to make sure it works, refs #3189

    Chris Fields authored
  2. test post-receive hook, post-SSL

    Chris Fields authored
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