| 2013-09-03 |
Chris Fields | some more README tweaks
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| 2013-09-03 |
Chris Fields | a few mroe markdown bits
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | create README.md file
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | create README.md file
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | add back perl versions
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | remove branch from testing
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | Merge branch 'topic/travis-scripts'
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | another fix (related ID)
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | fix remote DB test
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | remove obsolete branch from testing
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'v1_cherry' into v1
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add 5.18 for branch
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add v1_cherry
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | get test passing in cases where Error not installed
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | fix remote reversal of order bug
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add back mising tests from master
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Correct regexp on line 131, all tests pass
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| 2013-09-02 |
Brian Osborne | Minor doc change
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Minor doc change
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | [no ci] remove before_scripts section, will rework...
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| 2013-09-02 |
Chris Fields | bah, add back Bio::Root::Root
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| 2013-09-02 |
Chris Fields | remove Bio::DB::Sam for now, will move testing to a...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | try moving to before_install section, git commands...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | retest samtools (may be bad git path)
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | try a git checkout of the branch instead
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | test a samtools install from github tarball
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | test out samtools .deb instead; if this works, maybe...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add comment on Bio::ASN1::EntrezGene fussiness
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add bit on hash randomization and a few extras
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add bit on hash randomization and a few extras
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | tweak TODO message
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commit | commitdiff | tree |
| 2013-09-02 |
Florent Angly | Use 'exists', not 'defined', to check for existence...
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commit | commitdiff | tree |
| 2013-09-02 |
Florent Angly | Test fixes for Bio::Assembly::Tools::ContigSpectrum
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | hash randomization problem when mixing args with and...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | it does not make sense to warn about a requirement...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add TODO for this one, bug seems to affect position...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | sort the returned values for test purposes; order of...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add bug #
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | TODO some of the Assembly tests breaking from hash...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | fix for hash randomization bug in Bio::Map for perl...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'master' of git://github.com/fschwach...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | move hard-coded FT line length to a global
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'topic/pull_request47_adsj'
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'master' of git://github.com/adsj/bioperl...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge pull request #60 from MattOates/master
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'bugfix-exonerate' of git://github.com...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'master' of git://github.com/viklund/bioperl...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'master' of git://github.com/viklund/bioperl...
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commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | fix POD syntax
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commit | commitdiff | tree |
| 2013-09-02 |
Matt Oates | Added script to cut subsequences out of a set of sequence...
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commit | commitdiff | tree |
| 2013-09-02 |
Matt Oates | Added script for breaking sequence files into equal...
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commit | commitdiff | tree |
| 2013-09-02 |
antony03 | FastAlign.pl
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Fix warning, 'inclusion threshold'
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commit | commitdiff | tree |
| 2013-09-02 |
Florent Angly | Fixed some "undefined value" warnings when taxonomy...
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commit | commitdiff | tree |
| 2013-09-02 |
Jean-Frédéric Berthelot | Add unit test for SearchIO::Exonerate negative score...
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commit | commitdiff | tree |
| 2013-09-02 |
Jean-Frédéric Berthelot | Fix bug with score parsing in SearchIO::Exonerate
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Sorry about this, analyzing new output files is leading...
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Minor regex change
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Remove unused
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Corrected, all SearchIO tests pass
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Back this out, related tests are failing
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Add strand() so nhmmer can get strand data
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Add partial support for nhmmer (version 3.1)
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commit | commitdiff | tree |
| 2013-07-12 |
Lincoln Stein | add version number to LoadHelper
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commit | commitdiff | tree |
| 2013-07-12 |
Lincoln Stein | dramatically improve performance when loading multiple...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed bug where not all nodes in lineage were merged...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | More tests
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Better distinguish ambiguous taxon names
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed issue where ambiguous taxa names got the same...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed bug where taxon rank was missing
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | More Bio::DB::Taxonomy::list tests
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Boolean return status for merge_lineage()
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed number of tests in t/ClusterIO/SequenceFamily.t
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed use of uninitialized value $reporttype
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed redefined variable
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Small POD and and error message change
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Adding arbitrary branch length in Bio::DB::Taxonomy...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Use a default format for as_string
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Test uses species, not intermediary node
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Avoid use of an undefined value as an ARRAY reference
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Use list context instead of scalar context to include...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed POD indentation
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Tests for Bio::Taxonomy::get_tree
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commit | commitdiff | tree |
| 2013-07-12 |
Chris Fields | update tests for perl 5.18
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commit | commitdiff | tree |
| 2013-07-12 |
hyphaltip | make explicit
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commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Bug 3415
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commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | maint: remove hard tabs and trailing whitespace
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commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Merge branch 'master' of github.com:bioperl/bioperl...
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commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Add dna_to_aa_aln method and tests
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commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | Annotation: fix typo on test
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commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | Bio::Cluster::SequenceFamily - bug fixes and performance
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commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Add support for version 4, all tests pass
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commit | commitdiff | tree |
| 2013-07-11 |
hyphaltip | missing request for marker name in the call
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | recover GenericWebAgent from Bio-EUtilities
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commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | Per: http://www.bioperl.org/wiki/Bioperl_Best_Practices and
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commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | fix conflict
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commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | typo, removed ->
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commit | commitdiff | tree |
| 2013-07-11 |
Brian Osborne | Bio::AlignIO::fasta was not always using />\s*(\S+...
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commit | commitdiff | tree |
| 2013-07-11 |
Francisco J. Ossandon | Fix for Bug #3251, plus fixed a couple of regular expression...
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commit | commitdiff | tree |
| 2013-07-11 |
Francisco J. Ossandon | Revert "Fixed no-hit blast bug and faulty regexs, added...
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