| 2013-09-02 |
Chris Fields | remove obsolete branch from testing
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'v1_cherry' into v1
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add 5.18 for branch
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add v1_cherry
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | get test passing in cases where Error not installed
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | fix remote reversal of order bug
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add back mising tests from master
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Correct regexp on line 131, all tests pass
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Minor doc change
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Minor doc change
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | [no ci] remove before_scripts section, will rework...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | bah, add back Bio::Root::Root
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | remove Bio::DB::Sam for now, will move testing to a...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | try moving to before_install section, git commands...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | retest samtools (may be bad git path)
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | try a git checkout of the branch instead
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | test a samtools install from github tarball
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | test out samtools .deb instead; if this works, maybe...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add comment on Bio::ASN1::EntrezGene fussiness
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add bit on hash randomization and a few extras
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add bit on hash randomization and a few extras
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | tweak TODO message
|
commit | commitdiff | tree |
| 2013-09-02 |
Florent Angly | Use 'exists', not 'defined', to check for existence...
|
commit | commitdiff | tree |
| 2013-09-02 |
Florent Angly | Test fixes for Bio::Assembly::Tools::ContigSpectrum
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | hash randomization problem when mixing args with and...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | it does not make sense to warn about a requirement...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add TODO for this one, bug seems to affect position...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | sort the returned values for test purposes; order of...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | add bug #
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | TODO some of the Assembly tests breaking from hash...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | fix for hash randomization bug in Bio::Map for perl...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'master' of git://github.com/fschwach...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | move hard-coded FT line length to a global
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'topic/pull_request47_adsj'
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'master' of git://github.com/adsj/bioperl...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge pull request #60 from MattOates/master
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'bugfix-exonerate' of git://github.com...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'master' of git://github.com/viklund/bioperl...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | Merge branch 'master' of git://github.com/viklund/bioperl...
|
commit | commitdiff | tree |
| 2013-09-02 |
Chris Fields | fix POD syntax
|
commit | commitdiff | tree |
| 2013-09-02 |
Matt Oates | Added script to cut subsequences out of a set of sequence...
|
commit | commitdiff | tree |
| 2013-09-02 |
Matt Oates | Added script for breaking sequence files into equal...
|
commit | commitdiff | tree |
| 2013-09-02 |
antony03 | FastAlign.pl
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Fix warning, 'inclusion threshold'
|
commit | commitdiff | tree |
| 2013-09-02 |
Florent Angly | Fixed some "undefined value" warnings when taxonomy...
|
commit | commitdiff | tree |
| 2013-09-02 |
Jean-Frédéric Berthelot | Add unit test for SearchIO::Exonerate negative score...
|
commit | commitdiff | tree |
| 2013-09-02 |
Jean-Frédéric Berthelot | Fix bug with score parsing in SearchIO::Exonerate
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Sorry about this, analyzing new output files is leading...
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Minor regex change
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Remove unused
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Corrected, all SearchIO tests pass
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Back this out, related tests are failing
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Add strand() so nhmmer can get strand data
|
commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Add partial support for nhmmer (version 3.1)
|
commit | commitdiff | tree |
| 2013-07-12 |
Lincoln Stein | add version number to LoadHelper
|
commit | commitdiff | tree |
| 2013-07-12 |
Lincoln Stein | dramatically improve performance when loading multiple...
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed bug where not all nodes in lineage were merged...
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | More tests
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Better distinguish ambiguous taxon names
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed issue where ambiguous taxa names got the same...
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed bug where taxon rank was missing
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | More Bio::DB::Taxonomy::list tests
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Boolean return status for merge_lineage()
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed number of tests in t/ClusterIO/SequenceFamily.t
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed use of uninitialized value $reporttype
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed redefined variable
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Small POD and and error message change
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Adding arbitrary branch length in Bio::DB::Taxonomy...
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Use a default format for as_string
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Test uses species, not intermediary node
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Avoid use of an undefined value as an ARRAY reference
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Use list context instead of scalar context to include...
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed POD indentation
|
commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Tests for Bio::Taxonomy::get_tree
|
commit | commitdiff | tree |
| 2013-07-12 |
Chris Fields | update tests for perl 5.18
|
commit | commitdiff | tree |
| 2013-07-12 |
hyphaltip | make explicit
|
commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Bug 3415
|
commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | maint: remove hard tabs and trailing whitespace
|
commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Merge branch 'master' of github.com:bioperl/bioperl...
|
commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Add dna_to_aa_aln method and tests
|
commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | Annotation: fix typo on test
|
commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | Bio::Cluster::SequenceFamily - bug fixes and performance
|
commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Add support for version 4, all tests pass
|
commit | commitdiff | tree |
| 2013-07-11 |
hyphaltip | missing request for marker name in the call
|
commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | recover GenericWebAgent from Bio-EUtilities
|
commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | Per: http://www.bioperl.org/wiki/Bioperl_Best_Practices and
|
commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | fix conflict
|
commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | typo, removed ->
|
commit | commitdiff | tree |
| 2013-07-11 |
Brian Osborne | Bio::AlignIO::fasta was not always using />\s*(\S+...
|
commit | commitdiff | tree |
| 2013-07-11 |
Francisco J. Ossandon | Fix for Bug #3251, plus fixed a couple of regular expression...
|
commit | commitdiff | tree |
| 2013-07-11 |
Francisco J. Ossandon | Revert "Fixed no-hit blast bug and faulty regexs, added...
|
commit | commitdiff | tree |
| 2013-07-11 |
unknown | Fixed no-hit blast bug and faulty regexs, added tests
|
commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | Bio::Perl - fix indentation (remove tabs, and weird...
|
commit | commitdiff | tree |
| 2013-07-11 |
Paul Cantalupo | updating Changes file
|
commit | commitdiff | tree |
| 2013-07-11 |
Paul Cantalupo | Merge branch 'topic/bug3302'
|
commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | Don't use a separate default scalar when there's a...
|
commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | follow perl recommendations:
|
commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | fix indentation (remove tabs, and weird 3 spaces indentation)
|
commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | follow perl recommendations:
|
commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | use until instead of while(1){last if...}
|
commit | commitdiff | tree |
