| 2013-12-18 |
Chris Fields | skip Bio::ASN1::EntrezGene check (circ dependency fixed...
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | [skip ci] add some changes
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | bump versions prior to merge
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | IndexedBase.pm: Fixed an undefined warning
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Build.PL: A change in latest Module::Build version...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | SeqFeature.t: Added an explicit DESTROY for $dbfa,...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/DB/SeqFeature/Store/Loader.pm: Expanded DESTROY...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | berkeleydb.pm: Added the missing removal of parentage_db...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | SQLite.pm: Add the tracking of the file database location,
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | IndexedBase.pm: Adding the close of filehandles and...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | LocalDB/Fasta.t: Removing leftover temporal files.
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | BioDBGFF.t: Most of the tests can be handled fine by...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | LoadHelper.pm: Some temporal files are not deleted...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SearchIO/SearchResultEventBuilder.pm: Avoid adding...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/Index/Fasta.pm: Removed a fixed offset adjustment...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/DB/Flat/BDB.pm: Windows offset adjustment code...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio::SeqIO::fasta.pm: Replace chomp for s/// since...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SearchIO/Blast.pm: Removed tabs
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SearchIO/blast.pm: Fixed bug #2978. Added a code...
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | Revert "test failing build"
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | test failing build
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | test Bio::ASN1::EntrezGene
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | see if we can get travis-ci notifications working
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commit | commitdiff | tree |
| 2013-12-18 |
Carnë Draug | Bio::Align::Utilities - remove usage of /r option to...
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commit | commitdiff | tree |
| 2013-12-18 |
Carnë Draug | Fix nonsense in code comments.
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commit | commitdiff | tree |
| 2013-12-18 |
Carnë Draug | Bio::Align::Utilities - follow some perl best practices.
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commit | commitdiff | tree |
| 2013-12-18 |
Carnë Draug | Bio::Align::Utilities - new function most_common_sequences
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commit | commitdiff | tree |
| 2013-12-18 |
Carnë Draug | Bio::SimpleAlign - follow some perl best practices
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SeqIO/interpro.pm: Recognition of '<protein>' is...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Removed tabs from previous commit
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SimpleAlign.pm: Fixed a TODO, allowed the use of...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Untabified 't/LocalDB/Index/Index.t' and deleted some...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Big Windows compatibility fixes. Now all tests pass...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/Index/Blast: Fixed _index_file to adjust filehandle...
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| 2013-12-18 |
Francisco J. Ossandon | Bio/SearchIO/blasttable: Recover conserved value from...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/Assembly/Singlet: Get End from parent sequence...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/Index/Abstract: Fixed uninitialized warning from...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Merge pull request #54 from fjossandon/master
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SeqFeature/Generic.pm: Fixed uninitialized warnings
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | t/SeqFeature/Generic.t: Fixed a test of circular sequences...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SeqFeature/Generic.pm: Updated Start, End and Length...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Merge remote branch 'upstream/master' into test
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/DB/Fasta.pm: Small Windows compatibility fix in...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SeqFeatureI.pm: Changes to spliced_seq sequence...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/Factory/FTLocationFactory.pm: Refined logic for...
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commit | commitdiff | tree |
| 2013-12-18 |
Florent Angly | BigInt and BigFloat commented out. Commenting them...
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commit | commitdiff | tree |
| 2013-12-18 |
Florent Angly | Math::Random does not seem to be used anywhere... removing it
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commit | commitdiff | tree |
| 2013-12-18 |
Florent Angly | Better error message
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commit | commitdiff | tree |
| 2013-12-18 |
Dave Messina | Bugfix: wasn't checking return value from _load_module...
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commit | commitdiff | tree |
| 2013-12-18 |
Dave Messina | Adding script which runs deob_index to update the db...
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commit | commitdiff | tree |
| 2013-12-18 |
Dave Messina | Updating Bug address. Adding -w to perl invocation.
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | fix issue with seq_id when set to 0, patch courtesy...
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | add support for a stricter standard codon table, for...
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | add some additional comments
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | fix NCBIHelper bug, vars => ours
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | remove and refactor genbank CONTIG code, address part...
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | clean up code
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | add test case for GenBank tests for bug #3448
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commit | commitdiff | tree |
| 2013-12-18 |
Brian Osborne | Fix to alignment regex
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/PrimarySeq.pm: Fixed some 'uninitialized value...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/SeqUtils: trunc_with_features() and revcom_with_features()
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Fix typing errors
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commit | commitdiff | tree |
| 2013-12-18 |
Brian Osborne | Reformatting and editing
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | FTLocationFactory.pm: Fix in from_string() for some...
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | forgot to be on topic
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | No, really, fix the conflict :P
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | PrimarySeqI.pm: Avoid using Bio::Root::clone when object
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commit | commitdiff | tree |
| 2013-12-18 |
Chris Fields | add branch to track commits
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commit | commitdiff | tree |
| 2013-12-18 |
Brian Osborne | Set the EUtils URL in NCBIHelper, inherit in entrez...
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commit | commitdiff | tree |
| 2013-09-16 |
Chris Fields | change eutil URL
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commit | commitdiff | tree |
| 2013-09-14 |
Chris Fields | update Changes
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commit | commitdiff | tree |
| 2013-09-14 |
Brian Osborne | Change regexp to handle degenerate chars, all tests...
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commit | commitdiff | tree |
| 2013-09-12 |
Chris Fields | minor version bump
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commit | commitdiff | tree |
| 2013-09-12 |
Chris Fields | some ambiguity issues with this method call for some...
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commit | commitdiff | tree |
| 2013-09-11 |
Chris Fields | chmod of Build.PL to not be exe
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commit | commitdiff | tree |
| 2013-09-11 |
Chris Fields | update Changes
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commit | commitdiff | tree |
| 2013-09-11 |
Chris Fields | bump version
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commit | commitdiff | tree |
| 2013-09-10 |
Chris Fields | skip tests if the cloning class used happens to be...
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commit | commitdiff | tree |
| 2013-09-10 |
Chris Fields | Don't compare floats directly; make range of comparisons...
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commit | commitdiff | tree |
| 2013-09-08 |
Chris Fields | bump to a better version, not like we will use the...
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commit | commitdiff | tree |
| 2013-09-08 |
Chris Fields | bump version, remove Bio-Biblio collision
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commit | commitdiff | tree |
| 2013-09-08 |
Carnë Draug | split Bio-Biblio into a separate distribution
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commit | commitdiff | tree |
| 2013-09-07 |
Chris Fields | remove multi-declaration warning
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commit | commitdiff | tree |
| 2013-09-07 |
hyphaltip | remove multi-declare variable warning
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commit | commitdiff | tree |
| 2013-09-07 |
Chris Fields | Bio::SeqFeature::Annotated is dead
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commit | commitdiff | tree |
| 2013-09-07 |
Chris Fields | Bio::SF::Annotated is deprecated
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commit | commitdiff | tree |
| 2013-09-07 |
Chris Fields | remove Bio-Root since this branch still has it
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commit | commitdiff | tree |
| 2013-09-07 |
Chris Fields | fix skip miscounts
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commit | commitdiff | tree |
| 2013-09-07 |
Chris Fields | remove Bio::ASN1::EntrezGene from tests, this still...
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commit | commitdiff | tree |
| 2013-09-04 |
Chris Fields | skip tests if Bio::DB::Sam is present but samtools...
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commit | commitdiff | tree |
| 2013-09-04 |
Chris Fields | bump version
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | add local branch to travis-ci
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commit | commitdiff | tree |
| 2013-09-03 |
Chris Fields | some more README tweaks
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commit | commitdiff | tree |
| 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 |
