| 2010-08-03 |
Chris Fields | [bug 2984] end was calculated based on arbitrary symbols...
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commit | commitdiff | tree |
| 2010-08-03 |
Chris Fields | strand should be defined in a comparison
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| 2010-08-03 |
Chris Fields | [bug 2982] score<->percID mixup, patch courtesy Alexei...
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commit | commitdiff | tree |
| 2010-08-03 |
Chris Fields | make sure the returned format is GFF3
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commit | commitdiff | tree |
| 2010-08-03 |
Chris Fields | updates
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commit | commitdiff | tree |
| 2010-08-03 |
Chris Fields | move YAML to recommends
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commit | commitdiff | tree |
| 2010-08-03 |
Chris Fields | [bug 2725] some updates to tests so they actually test...
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commit | commitdiff | tree |
| 2010-08-02 |
Chris Fields | [bug 2599] add support for DBLINK output, by just allowing...
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commit | commitdiff | tree |
| 2010-08-02 |
Chris Fields | remove debugging
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commit | commitdiff | tree |
| 2010-07-30 |
Chris Fields | return the first note (scalar context of array, was...
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commit | commitdiff | tree |
| 2010-07-30 |
Chris Fields | [bug 3126] catch description (patch courtesy Toshihiko...
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| 2010-07-30 |
Chris Fields | [bug 3122] catch seek calls on the unseekable (thanks...
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| 2010-07-29 |
Robert Buels | strip keyword substitution from perl scripts
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commit | commitdiff | tree |
| 2010-07-29 |
Robert Buels | strip keyword substitution from perl modules
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commit | commitdiff | tree |
| 2010-07-29 |
Chris Fields | domain flag borking the request; fix courtesy John...
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commit | commitdiff | tree |
| 2010-07-29 |
John SJ Anderson | Expand how sequence features are rebuilt when objects...
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| 2010-07-29 |
John SJ Anderson | Introspect feature objects and call apporpriate GFF...
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| 2010-07-27 |
Chris Fields | * add tests for circular sequences
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| 2010-07-27 |
Chris Fields | ss-DNA is legit
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| 2010-07-27 |
Chris Fields | phiX174 sequence, for is_circular SF tests
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commit | commitdiff | tree |
| 2010-07-25 |
John SJ Anderson | silence exception that happens with -y option
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| 2010-07-23 |
Chris Fields | [RT 58464] patching to allow file names with spaces
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| 2010-07-23 |
Chris Fields | [RT 54702] patch symlink_script.pl, thanks to Curtis...
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| 2010-07-23 |
Chris Fields | Merge branch 'topic/cjfields_interpro_get_dbxref'
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| 2010-07-23 |
Chris Fields | remote db ID change causing fail
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| 2010-07-23 |
Chris Fields | test count off on skip (ID mapper appears to be having...
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commit | commitdiff | tree |
| 2010-07-23 |
Chris Fields | clean up generated index files
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commit | commitdiff | tree |
| 2010-07-23 |
Chris Fields | cleanup tests, passing but file cleanup not in place yet
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commit | commitdiff | tree |
| 2010-07-23 |
Chris Fields | move Bio::Assembly::IO tests into their own directory...
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commit | commitdiff | tree |
| 2010-07-23 |
Chris Fields | more fixes for warnings; tests are passing
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commit | commitdiff | tree |
| 2010-07-23 |
Jonathan "Duke"... | Add a test for get_references and to_string
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commit | commitdiff | tree |
| 2010-07-23 |
Jonathan "Duke"... | Add tests for class_list, get_examples and get_external_docu...
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commit | commitdiff | tree |
| 2010-07-23 |
Jonathan "Duke"... | Add some tests for get_members and protein_count and...
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commit | commitdiff | tree |
| 2010-07-22 |
Chris Fields | pinpointing the problem, perhaps, paint me perplexed
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commit | commitdiff | tree |
| 2010-07-22 |
Chris Fields | a bit o' debugging; alias add_dbxrefs to add_dbxref
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commit | commitdiff | tree |
| 2010-07-22 |
Chris Fields | use add_dbxrefs with contexts instead of the various...
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commit | commitdiff | tree |
| 2010-07-22 |
Chris Fields | reimplement various methods in terms of get_dbxrefs...
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commit | commitdiff | tree |
| 2010-07-22 |
Chris Fields | squash warnings popping up with uninit data; marked...
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commit | commitdiff | tree |
| 2010-07-20 |
Chris Fields | allow POST for ID lists longer than 200 or terms longer...
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commit | commitdiff | tree |
| 2010-07-16 |
Chris Fields | [bug 3095] doc changes to indicate difference between...
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commit | commitdiff | tree |
| 2010-07-16 |
Chris Fields | tests skipped off by 3, fixed
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commit | commitdiff | tree |
| 2010-07-16 |
Chris Fields | remote data change; make test more flexible
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commit | commitdiff | tree |
| 2010-07-16 |
Chris Fields | [bug 3107] pass strand info to alns
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commit | commitdiff | tree |
| 2010-07-05 |
Chris Fields | add some significant milestones
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commit | commitdiff | tree |
| 2010-07-03 |
Chris Fields | Merge branch 'topic/species_proxy'
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commit | commitdiff | tree |
| 2010-07-02 |
Chris Fields | test commit for org setup
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commit | commitdiff | tree |
| 2010-07-01 |
Chris Fields | fix edge case when adding gaps
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | squash warning
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | [bug 3014] passed values should be defined, default...
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| 2010-06-30 |
Chris Fields | add documentation on code move
Signed-off-by: Chris Fields <cjfields@bioperl.org>
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| 2010-06-30 |
Chris Fields | update MANIFEST
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| 2010-06-30 |
Chris Fields | remove dependencies
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | remove microarray-specific code into either bioperl...
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | make sure only defined values are passed on
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | fix skip test number
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | switch to Test::Weaken, optionally run
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | require, not use (I always screw that up)
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | move check for Leaktrace into BEGIN, then skip if needed
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commit | commitdiff | tree |
| 2010-06-29 |
Chris Fields | Merge branch 'master' into topic/species_proxy
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commit | commitdiff | tree |
| 2010-06-29 |
Chris Fields | remote database change (ensembl ID not present in mapper...
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commit | commitdiff | tree |
| 2010-06-29 |
Chris Fields | add ss-RNA to allowed moltypes
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commit | commitdiff | tree |
| 2010-06-29 |
Chris Fields | revert species to the prior version (all tests now...
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commit | commitdiff | tree |
| 2010-06-28 |
Chris Fields | clean up cleaning up (e.g. DESTROY properly)
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commit | commitdiff | tree |
| 2010-06-28 |
Chris Fields | add test for mem leak (may have to be modified)
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commit | commitdiff | tree |
| 2010-06-28 |
Chris Fields | bit premature to check for this (API indicates this...
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commit | commitdiff | tree |
| 2010-06-28 |
Chris Fields | remove code refs for index tests, a few doc changes...
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commit | commitdiff | tree |
| 2010-06-28 |
Chris Fields | Bio::Species delegates to Bio::Taxon and Bio::Tree...
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commit | commitdiff | tree |
| 2010-06-27 |
Chris Fields | catch refs that sneak through, such as during thread...
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commit | commitdiff | tree |
| 2010-06-26 |
Chris Fields | fix lower-case issue with moltype
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commit | commitdiff | tree |
| 2010-06-26 |
Chris Fields | update bad test check
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commit | commitdiff | tree |
| 2010-06-26 |
Chris Fields | fix error where, with protein seqs the division and...
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commit | commitdiff | tree |
| 2010-06-26 |
Chris Fields | protein molecule type not switched, correct bad test...
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | update MANIFEST
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | uncomment remove_dir() to cleanup files
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | move sub creation to BEGIN, and document the _dclone...
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | update MANIFEST
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | overhaul Root::clone to use either Clone, Storable...
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commit | commitdiff | tree |
| 2010-06-24 |
Chris Fields | move clone() method from TreeFunctionsI to Tree, as...
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commit | commitdiff | tree |
| 2010-06-24 |
Chris Fields | silence warnings with a default of 0
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commit | commitdiff | tree |
| 2010-06-24 |
Chris Fields | make this a real-world example
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commit | commitdiff | tree |
| 2010-06-22 |
Chris Fields | fix conflict
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commit | commitdiff | tree |
| 2010-06-22 |
Warren Kretzschmar | Bio/SeqIO/msout.pm 1.1.5
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commit | commitdiff | tree |
| 2010-06-22 |
Warren Kretzschmar | Bio/SeqIO/msout.pm 1.1.4
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commit | commitdiff | tree |
| 2010-06-22 |
Warren Kretzschmar | Bio/SeqIO/msout.pm 1.1.3
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commit | commitdiff | tree |
| 2010-06-22 |
Jay Hannah | Works great in Bio::DB::SeqFeature::Store::DBI::SQLite...
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commit | commitdiff | tree |
| 2010-06-22 |
Florent Angly | More robust creation of cross-contigs
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commit | commitdiff | tree |
| 2010-06-22 |
Florent Angly | Removed temporary debugging code
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commit | commitdiff | tree |
| 2010-06-22 |
Florent Angly | Fixed typos in Bio::Assembly::Contig
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commit | commitdiff | tree |
| 2010-06-14 |
Naama Menda | added 'xref' identifier recognition for obo files....
Signed-off-by: Chris Fields <cjfields@bioperl.org>
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commit | commitdiff | tree |
| 2010-06-14 |
Warren Kretzschmar | Bio/SeqIO/msout.pm 1.1.3
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commit | commitdiff | tree |
| 2010-06-11 |
Chris Fields | [bug 3099] initial msout Seq parser, courtesy Warren...
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commit | commitdiff | tree |
| 2010-06-10 |
Chris Fields | Ben's changes to fix bug with file, along with comment...
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | [bug 3028] some rearrangement for FigTree output
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | Merge branch 'topic/bug3089'
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | [bug 3089] iteration and found_again added to GenericHit...
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | small tweak to add for Args in docs
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | add is_remote docs from Bio::LocationI to Atomic and...
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | expected answer off by two (frameshift
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | more cleanup of methods
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | move seq offset calc into a separate method
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