| 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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| 2014-03-27 |
Francisco J. Ossandon | Merge pull request #66 from nathanweeks/sqlite_collate_nocase
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| 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, "$hit->length" method...
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| 2014-01-13 |
Francisco J. Ossandon | HMMER: Added support of CS lines in Hmmer2 outputs...
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commit | commitdiff | tree |
| 2014-01-13 |
Francisco J. Ossandon | Hmmer2: Removed code redundancy by merging the parsing of
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commit | commitdiff | tree |
| 2014-01-11 |
Francisco J. Ossandon | Hmmer2: Now "$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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| 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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commit | commitdiff | tree |
| 2013-12-17 |
Francisco J. Ossandon | IndexedBase.pm: Adding the close of filehandles and...
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commit | commitdiff | tree |
| 2013-12-15 |
Francisco J. Ossandon | LocalDB/Fasta.t: Removing leftover temporal files.
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commit | commitdiff | tree |
| 2013-12-15 |
Francisco J. Ossandon | BioDBGFF.t: Most of the tests can be handled fine by...
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commit | commitdiff | tree |
| 2013-12-15 |
Francisco J. Ossandon | LoadHelper.pm: Some temporal files are not deleted...
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commit | commitdiff | tree |
| 2013-12-11 |
Francisco J. Ossandon | Bio/SearchIO/SearchResultEventBuilder.pm: Avoid adding...
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commit | commitdiff | tree |
| 2013-12-10 |
Francisco J. Ossandon | Bio/Index/Fasta.pm: Removed a fixed offset adjustment...
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commit | commitdiff | tree |
| 2013-12-10 |
Francisco J. Ossandon | Bio/DB/Flat/BDB.pm: Windows offset adjustment code...
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commit | commitdiff | tree |
| 2013-12-06 |
Francisco J. Ossandon | Bio::SeqIO::fasta.pm: Replace chomp for s/// since...
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commit | commitdiff | tree |
| 2013-12-04 |
Francisco J. Ossandon | Bio/SearchIO/Blast.pm: Removed tabs
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commit | commitdiff | tree |
| 2013-12-04 |
Francisco J. Ossandon | Bio/SearchIO/blast.pm: Fixed bug #2978. Added a code...
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commit | commitdiff | tree |
| 2013-11-25 |
Francisco J. Ossandon | Bio/SeqIO/interpro.pm: Recognition of '<protein>' is...
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commit | commitdiff | tree |
| 2013-11-23 |
Francisco J. Ossandon | Removed tabs from previous commit
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commit | commitdiff | tree |
| 2013-11-23 |
Francisco J. Ossandon | Bio/SimpleAlign.pm: Fixed a TODO, allowed the use of...
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commit | commitdiff | tree |
| 2013-11-22 |
Francisco J. Ossandon | Untabified 't/LocalDB/Index/Index.t' and deleted some...
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commit | commitdiff | tree |
| 2013-11-22 |
Francisco J. Ossandon | Big Windows compatibility fixes. Now all tests pass...
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commit | commitdiff | tree |
| 2013-11-21 |
Francisco J. Ossandon | Bio/Index/Blast: Fixed _index_file to adjust filehandle...
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commit | commitdiff | tree |
| 2013-11-21 |
Francisco J. Ossandon | Bio/SearchIO/blasttable: Recover conserved value from...
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commit | commitdiff | tree |
| 2013-11-21 |
Francisco J. Ossandon | Bio/Assembly/Singlet: Get End from parent sequence...
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commit | commitdiff | tree |
| 2013-11-21 |
Francisco J. Ossandon | Bio/Index/Abstract: Fixed uninitialized warning from...
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commit | commitdiff | tree |
| 2013-11-20 |
Francisco J. Ossandon | Merge pull request #54 from fjossandon/master
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commit | commitdiff | tree |
| 2013-11-11 |
Francisco J. Ossandon | Bio/SeqFeature/Generic.pm: Fixed uninitialized warnings
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commit | commitdiff | tree |
| 2013-11-11 |
Francisco J. Ossandon | t/SeqFeature/Generic.t: Fixed a test of circular sequences...
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commit | commitdiff | tree |
| 2013-11-11 |
Francisco J. Ossandon | Bio/SeqFeature/Generic.pm: Updated Start, End and Length...
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