| 2014-08-04 |
Francisco J. Ossandon | Bio/SeqFeature/Generic.pm: Fix for issue #76, adjusted...
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commit | commitdiff | tree |
| 2014-08-01 |
Francisco J. Ossandon | all "nexml.pm": Fixed subroutines calling "Bio::Phylo...
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commit | commitdiff | tree |
| 2014-08-01 |
Francisco J. Ossandon | t/Tree/TreeIO/nexml.t: A close function was being used on
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commit | commitdiff | tree |
| 2014-07-31 |
Francisco J. Ossandon | hmmer.t: Added tests to document "$hit->bits"
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commit | commitdiff | tree |
| 2014-07-31 |
Francisco J. Ossandon | HMMERHSP: For HMMer report parsing, changed "$hsp-...
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commit | commitdiff | tree |
| 2014-07-31 |
Francisco J. Ossandon | Merge branch 'master' of https://github.com/bioperl...
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commit | commitdiff | tree |
| 2014-07-31 |
Francisco J. Ossandon | genbank.pm: Another tweak to "_read_GenBank_Species...
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commit | commitdiff | tree |
| 2014-06-27 |
Francisco J. Ossandon | genbank.pm: in "_read_GenBank_Species", adjusted a...
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commit | commitdiff | tree |
| 2014-06-27 |
Francisco J. Ossandon | Location/Split: Added its own "length" subroutine to
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commit | commitdiff | tree |
| 2014-06-08 |
Francisco J. Ossandon | (Thomas Sibley): Tell Storable to freeze and thaw CODE...
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commit | commitdiff | tree |
| 2014-06-02 |
Francisco J. Ossandon | Splicedseq.t: Reorganized new tests to use "-requires_networ...
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commit | commitdiff | tree |
| 2014-06-02 |
Stuart Archer | Add tests for spliced_seq remote sequence handling
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commit | commitdiff | tree |
| 2014-06-02 |
Stuart Archer | Fixed bug: too many Ns added by spliced_seq
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commit | commitdiff | tree |
| 2014-05-16 |
Francisco J. Ossandon | SeqFeature/Location.t: Added tests for GitHub issue...
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commit | commitdiff | tree |
| 2014-05-16 |
Francisco J. Ossandon | Merge pull request #71 from nathanweeks/issue/bio-seqfeature...
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commit | commitdiff | tree |
| 2014-05-08 |
Francisco J. Ossandon | SeqFeatureI.pm: Cleaned tabs, format and trailing whitespaces
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commit | commitdiff | tree |
| 2014-05-08 |
Francisco J. Ossandon | SeqFeatureI.pm: Splitted some very long lines and added...
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commit | commitdiff | tree |
| 2014-05-08 |
Francisco J. Ossandon | Merge pull request #67 from stu2/master
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commit | commitdiff | tree |
| 2014-05-08 |
Francisco J. Ossandon | Merge pull request #68 from tsibley/readline-return...
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| 2014-05-02 |
Francisco J. Ossandon | Updated INSTALL.WIN to the most recent document from...
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commit | commitdiff | tree |
| 2014-05-02 |
Francisco J. Ossandon | Added a missing module (XML::LibXML) in "recommended"
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commit | commitdiff | tree |
| 2014-05-01 |
Francisco J. Ossandon | Added some changes and bugfixes
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commit | commitdiff | tree |
| 2014-05-01 |
Francisco J. Ossandon | Build.PL: Demoted 'DB_File' status from "required" to
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commit | commitdiff | tree |
| 2014-04-30 |
Francisco J. Ossandon | RemoteBlast_rpsblast.t: Fixed a few number of skipped...
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commit | commitdiff | tree |
| 2014-04-30 |
Francisco J. Ossandon | Taxonomy.t: Added missing 'DB_File' requirement
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commit | commitdiff | tree |
| 2014-04-30 |
Francisco J. Ossandon | RandomFactory.t: Removed unused dependency "Math::Random",
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commit | commitdiff | tree |
| 2014-04-29 |
Francisco J. Ossandon | RemoteBlast.t: Fixed several number of skipped tests,
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commit | commitdiff | tree |
| 2014-04-29 |
Francisco J. Ossandon | BioFetch.t & SwissProt.t: Fixed some number of skipped...
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commit | commitdiff | tree |
| 2014-04-29 |
Francisco J. Ossandon | Added 'Data::Stag' requirement to many tests files
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commit | commitdiff | tree |
| 2014-04-29 |
Francisco J. Ossandon | Changed argument "requires_modules" to "require_module"
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commit | commitdiff | tree |
| 2014-04-28 |
Francisco J. Ossandon | Several LocalDB tests were failing for Windows' ActivePerl,
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commit | commitdiff | tree |
| 2014-04-28 |
Francisco J. Ossandon | Added 'DB_File' requirement to some tests files that...
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commit | commitdiff | tree |
| 2014-04-22 |
Francisco J. Ossandon | Standardized URL to "https://github.com/bioperl/bioperl...
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commit | commitdiff | tree |
| 2014-03-27 |
Francisco J. Ossandon | Merge pull request #66 from nathanweeks/sqlite_collate_nocase
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commit | commitdiff | tree |
| 2014-03-15 |
Francisco J. Ossandon | SeqIO/embl.pm: At 'next_seq' subroutine, added a little...
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commit | commitdiff | tree |
| 2014-03-07 |
Francisco J. Ossandon | SeqIO/Genbank: Complete elimination of the use of ...
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commit | commitdiff | tree |
| 2014-03-06 |
Francisco J. Ossandon | Unflattener: Fix for Bug #3458. Incorporated Bastien...
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commit | commitdiff | tree |
| 2014-03-06 |
Francisco J. Ossandon | SeqIO/Tinyseq.pm: Fixed an uninitialized value warning...
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commit | commitdiff | tree |
| 2014-03-04 |
Francisco J. Ossandon | SearchResultEventBuilder: Simplified calculation of...
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commit | commitdiff | tree |
| 2014-03-04 |
Francisco J. Ossandon | Bio/Ontology/InterProTerm: Fixed an uninitialized warning in
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commit | commitdiff | tree |
| 2014-03-04 |
Francisco J. Ossandon | SeqFeatureDB Postgres: Changed the use of system("cp...
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commit | commitdiff | tree |
| 2014-02-28 |
Francisco J. Ossandon | Massive check of file open lines. Changed bareword...
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commit | commitdiff | tree |
| 2014-02-25 |
Francisco J. Ossandon | Merge pull request #65 from MartinMcGrath/master
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commit | commitdiff | tree |
| 2014-02-04 |
Francisco J. Ossandon | Added back die message
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commit | commitdiff | tree |
| 2014-02-04 |
Francisco J. Ossandon | Propagated leftover changes from v1.6.x
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commit | commitdiff | tree |
| 2014-01-28 |
Francisco J. Ossandon | Updated Changes and minor cosmetical edits to blast.t
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commit | commitdiff | tree |
| 2014-01-28 |
Francisco J. Ossandon | Bio/SearchIO/blast: Treatment of Subject lines are...
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commit | commitdiff | tree |
| 2014-01-28 |
Francisco J. Ossandon | Merge pull request #63 from yschensandiego/patch-1
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commit | commitdiff | tree |
| 2014-01-28 |
Francisco J. Ossandon | Merge pull request #64 from yschensandiego/patch-2
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commit | commitdiff | tree |
| 2014-01-17 |
Francisco J. Ossandon | Hmmer3: When a hit description is too long, it is truncated in
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commit | commitdiff | tree |
| 2014-01-15 |
Francisco J. Ossandon | Added a test for Bio::Index::Hmmer at Index.t, which...
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commit | commitdiff | tree |
| 2014-01-14 |
Francisco J. Ossandon | Minor edit to Changes
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commit | commitdiff | tree |
| 2014-01-14 |
Francisco J. Ossandon | SearchResultEventBuilder & IteratedSearchResultEventBuilder:
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commit | commitdiff | tree |
| 2014-01-13 |
Francisco J. Ossandon | Update to Changes file with the latest fixes
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commit | commitdiff | tree |
| 2014-01-13 |
Francisco J. Ossandon | Hmmer3: For Hmmsearch and Hmmscan, "$hit->length" method...
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commit | commitdiff | tree |
| 2014-01-13 |
Francisco J. Ossandon | HMMER: Added support of CS lines in Hmmer2 outputs...
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commit | commitdiff | tree |
| 2014-01-13 |
Francisco J. Ossandon | Hmmer2: Removed code redundancy by merging the parsing of
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commit | commitdiff | tree |
| 2014-01-11 |
Francisco J. Ossandon | Hmmer2: Now "$result->query_length" and "$hit->length...
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commit | commitdiff | tree |
| 2014-01-10 |
Francisco J. Ossandon | Hmmer3: Added more query/hit length consistency checks...
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commit | commitdiff | tree |
| 2014-01-10 |
Francisco J. Ossandon | Hmmer2: Fixed a subtle bug where values set by a first...
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commit | commitdiff | tree |
| 2014-01-10 |
Francisco J. Ossandon | Hmmer2: Fixed a bug where "$hsp->{QUERY_LENGTH}" and
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commit | commitdiff | tree |
| 2014-01-09 |
Francisco J. Ossandon | Hmmer2: Added the recovery of the indentical and conserved...
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commit | commitdiff | tree |
| 2014-01-09 |
Francisco J. Ossandon | GenericHit: Changed "query_length" method behaviour...
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commit | commitdiff | tree |
| 2014-01-08 |
Francisco J. Ossandon | GenericHSP: Refined "_pre_gaps" to not use '.' for...
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commit | commitdiff | tree |
| 2014-01-08 |
Francisco J. Ossandon | infernal.t: Addition of '.' to gap symbols showed that...
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commit | commitdiff | tree |
| 2014-01-08 |
Francisco J. Ossandon | Hmmer3: Fixed wrong capture of homology line from alignment
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commit | commitdiff | tree |
| 2014-01-08 |
Francisco J. Ossandon | GenericHSP: Added '.' to gap symbols in "_pre_gaps",
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commit | commitdiff | tree |
| 2014-01-07 |
Francisco J. Ossandon | hmmer3: Major update to now fully support the parsing...
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commit | commitdiff | tree |
| 2014-01-06 |
Francisco J. Ossandon | Hmmer3: Added support to multi-query reports.
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commit | commitdiff | tree |
| 2014-01-06 |
Francisco J. Ossandon | Hmmer3: Added support to retrieve the CS line using
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commit | commitdiff | tree |
| 2014-01-06 |
Francisco J. Ossandon | Hmmer3: Parsing of HSP is broken if there is a result...
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commit | commitdiff | tree |
| 2014-01-06 |
Francisco J. Ossandon | Hmmer3: Final fix for Bug #3369. Eliminated the removal of
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commit | commitdiff | tree |
| 2014-01-05 |
Francisco J. Ossandon | Bio/SearchIO/hmmer3: Fix for Bug #3369. Added support...
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commit | commitdiff | tree |
| 2014-01-04 |
Francisco J. Ossandon | Bio/Map/Physical: Fixed "_calc_markerposition", which...
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commit | commitdiff | tree |
| 2013-12-31 |
Francisco J. Ossandon | CommandExts: My mistake, double-quotes in exe path...
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commit | commitdiff | tree |
| 2013-12-30 |
Francisco J. Ossandon | StandAloneBlast & CommandExts: Apply double-quotes on
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commit | commitdiff | tree |
| 2013-12-30 |
Francisco J. Ossandon | entrezgene: Fixed Bug #3453. Now code checks for multiple
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commit | commitdiff | tree |
| 2013-12-27 |
Francisco J. Ossandon | Windows use 'NUL' instead of '/dev/null', so added...
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commit | commitdiff | tree |
| 2013-12-24 |
Francisco J. Ossandon | Some cleaning of trailing spaces, added missing Changes
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commit | commitdiff | tree |
| 2013-12-24 |
Chris Fields | fix fussy test
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commit | commitdiff | tree |
| 2013-12-24 |
Francisco J. Ossandon | (from v1.6.x branch, missing from master)
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commit | commitdiff | tree |
| 2013-12-21 |
Francisco J. Ossandon | core.t: Removed the additional file extension of a...
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commit | commitdiff | tree |
| 2013-12-20 |
Francisco J. Ossandon | HIVQuery.t: Closed filehandle that was blocking deletion
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commit | commitdiff | tree |
| 2013-12-20 |
Francisco J. Ossandon | Taxonomy/flatfile.pm: Added DESTROY method to remove...
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commit | commitdiff | tree |
| 2013-12-19 |
Francisco J. Ossandon | Changed "cat" to "find" to be used as an example of
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commit | commitdiff | tree |
| 2013-12-19 |
Francisco J. Ossandon | hmmer.t: Fixed test that was using linux command "cat"
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commit | commitdiff | tree |
| 2013-12-19 |
Francisco J. Ossandon | RemoteBlast.t: Increased a little the delay between...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Consed.t: Removed the exclusion of Windows from the...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | HTTPget.t: Fixed a "bareword not allowed" error
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | MeSH.t: Updated test to expect the current description...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | MeSH.pm: A possible format change in the html content...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | WebDBSeqI.pm: Close a filehandle from an object that
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | BioFetch.pm: Close first the filehandle and then test...
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commit | commitdiff | tree |
| 2013-12-18 |
Francisco J. Ossandon | Bio/DB/TFBS/transfac_pro.pm: Added a DESTROY method...
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commit | commitdiff | tree |
| 2013-12-17 |
Francisco J. Ossandon | IndexedBase.pm: Fixed an undefined warning
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commit | commitdiff | tree |
| 2013-12-17 |
Francisco J. Ossandon | Build.PL: A change in latest Module::Build version...
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commit | commitdiff | tree |
| 2013-12-17 |
Francisco J. Ossandon | SeqFeature.t: Added an explicit DESTROY for $dbfa,...
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commit | commitdiff | tree |
| 2013-12-17 |
Francisco J. Ossandon | Bio/DB/SeqFeature/Store/Loader.pm: Expanded DESTROY...
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commit | commitdiff | tree |
| 2013-12-17 |
Francisco J. Ossandon | berkeleydb.pm: Added the missing removal of parentage_db...
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commit | commitdiff | tree |
| 2013-12-17 |
Francisco J. Ossandon | SQLite.pm: Add the tracking of the file database location,
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