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Commits on May 28, 2015
  1. @cjfields

    Merge pull request #15 from adsj/master

    cjfields authored
    Supply TEMPLATE and SUFFIX for temporary query sequence files.
Commits on May 26, 2015
  1. @adsj

    Supply TEMPLATE and SUFFIX for temporary query sequence files.

    adsj authored
    This avoid the problem of query sequence file names randomly ending
    in _Z, which makes (at least) wublastp (3.0SE-AB) try to unzgip the
    non-gzipped temporary file, resulting in an error.
Commits on Feb 20, 2015
  1. @carandraug

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

    carandraug authored
    …mport extra stuff into namespace
  2. @carandraug

    Merge pull request #13 from hettling/master

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

    removed obsolete whitespace

    hettling authored
Commits on Dec 18, 2014
  1. @fjossandon

    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. @fjossandon
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. @fjossandon

    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. @majensen
Commits on Aug 24, 2014
  1. @majensen

    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. @majensen
  3. @majensen
  4. @majensen

    fixed translate_params tests according to discussion at commit a6d0dc2;…

    majensen authored
    … removed TODO around translate_params test
Commits on Aug 23, 2014
  1. @majensen
  2. @majensen
  3. @majensen
Commits on Aug 22, 2014
  1. @fjossandon

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

    fjossandon authored
    to have been added by mistake
Commits on Jul 31, 2014
  1. @fjossandon
  2. @majensen
Commits on Jul 26, 2014
  1. @majensen
  2. @majensen

    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. @majensen

    fix parsing edge case

    majensen authored
  4. @majensen
Commits on Jul 24, 2014
  1. @fangly

    POD updates

    fangly authored
  2. @fangly
Commits on Jul 14, 2014
  1. @bosborne

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

    bosborne authored
    Add to documentation, reorganize code a bit
Commits on May 16, 2014
  1. @fjossandon

    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. @fjossandon

    Merge pull request #67 from stu2/master

    fjossandon authored
    Optimized speed of spliced_seq for local
  2. @fjossandon

    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. @fjossandon

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

    fjossandon authored
    and cleaned format and indentation
Commits on Apr 29, 2014
  1. @fjossandon

    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
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