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Commits on Feb 20, 2015
  1. Carnë Draug

    Raxml: use File::Spec->devnull() instead of our own code and do not i…

    carandraug authored
    …mport extra stuff into namespace
  2. Carnë Draug

    Merge pull request #13 from hettling/master

    carandraug authored
    yes, seems good.
Commits on Jan 31, 2015
  1. Chris Fields
  2. Chris Fields
Commits on Jan 28, 2015
  1. hettling

    removed obsolete whitespace

    hettling authored
Commits on Dec 18, 2014
  1. Francisco J. Ossandon

    StandAloneBlastPlus: Improved 'db_info' Algorithm ID regex,

    fjossandon authored
    which was failing in a test, and adjusted the mask maker programs
    (windowmasker, segmasker and dustmasker) to use 'maskinfo_asn1_text'
    output format, so it can be used with makeblastdb (all other formats
    fails). Removed the TODOs from the test file now that masking works.
  2. Francisco J. Ossandon
Commits on Oct 29, 2014
  1. hettling

    Added -d option (random starting tree) to raxml run, because raxml

    hettling authored
    complained about starting tree. Added test for -w option with tempdir().
    Test runs now.
  2. hettling

    (1) when -w option was provided with a custom directory, 'run' always

    hettling authored
    returned undef. This is now fixed. (2) When -quiet was set, redirection
    to /dev/null messed up the outfile name. This is also fixed.
Commits on Sep 1, 2014
  1. Francisco J. Ossandon

    WBCommandExts.t: Fixed a pending TODO related to

    fjossandon authored
    "->_translate_params" with the solution applied recently
    to BWA.t, Bowtie.t, Maq.t and Samtools.t
Commits on Aug 26, 2014
  1. Mark Jensen
Commits on Aug 24, 2014
  1. Mark Jensen

    no dependencies on any of the Test::* or Sub::Uplevel in any test (ex…

    majensen authored
    …cept maybe through Bio::Root::Test; in any case should not be frozen in the distro, but tests that break due to updates should instead be updated themselves.
  2. Mark Jensen
  3. Mark Jensen
  4. Mark Jensen

    fixed translate_params tests according to discussion at commit a6d0dc2;…

    majensen authored
    … removed TODO around translate_params test
Commits on Aug 23, 2014
  1. Mark Jensen
  2. Mark Jensen
  3. Mark Jensen
Commits on Aug 22, 2014
  1. Francisco J. Ossandon

    Removed empty file Bio/Tools/Run/hmmer3.pm, which seems

    fjossandon authored
    to have been added by mistake
Commits on Jul 31, 2014
  1. Francisco J. Ossandon
  2. Mark Jensen
Commits on Jul 26, 2014
  1. Mark Jensen
  2. Mark Jensen

    loosened validation for outfmt in BlastMethods to allow quoted multip…

    majensen authored
    …le values (new blast+ feature); added tests for issue 12 to SABlastPlus.t
  3. Mark Jensen

    fix parsing edge case

    majensen authored
  4. Mark Jensen
Commits on Jul 24, 2014
  1. Florent Angly

    POD updates

    fangly authored
  2. Florent Angly
Commits on Jul 14, 2014
  1. Brian Osborne

    Merge branch 'master' of github.com:bioperl/bioperl-live

    bosborne authored
    Add to documentation, reorganize code a bit
Commits on May 16, 2014
  1. Francisco J. Ossandon

    Merge pull request #71 from nathanweeks/issue/bio-seqfeature-lite-strand

    fjossandon authored
    Store Bio::SeqFeature::Lite strand correctly when "+", "-", or "."
Commits on May 8, 2014
  1. Francisco J. Ossandon

    Merge pull request #67 from stu2/master

    fjossandon authored
    Optimized speed of spliced_seq for local
  2. Francisco J. Ossandon

    Merge pull request #68 from tsibley/readline-return-undef

    fjossandon authored
    Always return undef from READLINE for EOF or failure
Commits on Apr 30, 2014
  1. Francisco J. Ossandon

    RemoteBlast_rpsblast.t: Fixed a few number of skipped tests,

    fjossandon authored
    and cleaned format and indentation
Commits on Apr 29, 2014
  1. Francisco J. Ossandon

    RemoteBlast.t: Fixed several number of skipped tests,

    fjossandon authored
    increased significantly server waiting cycle (sleep + retries)
    because server was taking much longer than current setting
    to return results, and cleaned format and indentation
Commits on Apr 21, 2014
Commits on Mar 27, 2014
  1. Francisco J. Ossandon

    Merge pull request #66 from nathanweeks/sqlite_collate_nocase

    fjossandon authored
    Use COLLATE NOCASE instead of LOWER() for Bio::DB::SeqFeature::Store::DBI::SQLite
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