| 2008-02-21 |
cjfields | add Graph::Directed to requirements for tests
|
commit | commitdiff | tree |
| 2008-02-21 |
cjfields | fix CUTG tests
|
commit | commitdiff | tree |
| 2008-02-21 |
cjfields | Now passes tests; added warnings for no returned exons...
|
commit | commitdiff | tree |
| 2008-02-20 |
cjfields | tests for bug 2453
|
commit | commitdiff | tree |
| 2008-02-20 |
cjfields | Bug 2453; needs tests
|
commit | commitdiff | tree |
| 2008-02-20 |
cjfields | Oops! Bug 2453 again.
|
commit | commitdiff | tree |
| 2008-02-20 |
cjfields | small fix for bug 2453, but see bugzilla for reasons...
|
commit | commitdiff | tree |
| 2008-02-20 |
cjfields | bug 2452
|
commit | commitdiff | tree |
| 2008-02-19 |
cjfields | TODO now works
|
commit | commitdiff | tree |
| 2008-02-13 |
cjfields | update interface documentation
|
commit | commitdiff | tree |
| 2008-02-13 |
cjfields | not 1.5.3 (modules don't work anymore)
|
commit | commitdiff | tree |
| 2008-02-12 |
cjfields | missing getter/setter added
|
commit | commitdiff | tree |
| 2008-02-12 |
cjfields | bug 2440
|
commit | commitdiff | tree |
| 2008-02-11 |
cjfields | remove comment (make sure tempfile/tempdirs stored...
|
commit | commitdiff | tree |
| 2008-02-11 |
cjfields | Fix for bug 2413. Shouldn't we delegate all IO-related...
|
commit | commitdiff | tree |
| 2008-02-10 |
cjfields | test commit msgs from /usr/local/bin
|
commit | commitdiff | tree |
| 2008-02-10 |
cjfields | checking svn post commits to list
|
commit | commitdiff | tree |
| 2008-02-07 |
cjfields | bug 2445: clean up hit table regex to skip N (Bernd...
|
commit | commitdiff | tree |
| 2008-02-05 |
cjfields | changed URL
|
commit | commitdiff | tree |
| 2008-02-05 |
cjfields | handles Bio::Taxon as well as Bio::Species now (might...
|
commit | commitdiff | tree |
| 2008-02-05 |
cjfields | * small rnamotif fix
|
commit | commitdiff | tree |
| 2008-02-05 |
cjfields | bug 2444 (HSP::significance returning wrong value)
|
commit | commitdiff | tree |
| 2008-02-05 |
cjfields | bug 2438; 'X' no longer completely ambiguous
|
commit | commitdiff | tree |
| 2008-02-05 |
cjfields | bug 2415
|
commit | commitdiff | tree |
| 2008-02-05 |
cjfields | bug 2442
|
commit | commitdiff | tree |
| 2008-02-04 |
cjfields | Fixed bits/raw_score issue related to GenericHit changes...
|
commit | commitdiff | tree |
| 2008-01-31 |
cjfields | bug 2436; add option for 'mismatch' (no match w/o gaps)
|
commit | commitdiff | tree |
| 2008-01-30 |
cjfields | Add simple method to retrieve parameter settings
|
commit | commitdiff | tree |
| 2008-01-25 |
cjfields | Returned value from EntrezGene is different
|
commit | commitdiff | tree |
| 2008-01-24 |
cjfields | Stefan's fix for entrezgene which includes a fix for...
|
commit | commitdiff | tree |
| 2008-01-22 |
cjfields | revert last commit; problem more serious than initially...
|
commit | commitdiff | tree |
| 2008-01-21 |
cjfields | get rid of annoying 'pseudohashes' error; tests now...
|
commit | commitdiff | tree |
| 2008-01-21 |
cjfields | Use db settings for both BioDBGFF and BioDBSeqFeature_mysql...
|
commit | commitdiff | tree |
| 2008-01-17 |
cjfields | remove format option for EMBL just in case...
|
commit | commitdiff | tree |
| 2008-01-17 |
cjfields | bug 2433
|
commit | commitdiff | tree |
| 2008-01-17 |
cjfields | Starter cross_match tests and sample data. Needs...
|
commit | commitdiff | tree |
| 2008-01-17 |
cjfields | Tentative fix for bug 2427
|
commit | commitdiff | tree |
| 2008-01-17 |
cjfields | bug 2423
|
commit | commitdiff | tree |
| 2008-01-17 |
cjfields | bug 2431
|
commit | commitdiff | tree |
| 2008-01-15 |
cjfields | Bug 2426
|
commit | commitdiff | tree |
| 2008-01-14 |
cjfields | test post-commit after fsfs transfer (2nd try)
|
commit | commitdiff | tree |
| 2008-01-14 |
cjfields | test commits after fsfs transfer
|
commit | commitdiff | tree |
| 2008-01-07 |
cjfields | Test
|
commit | commitdiff | tree |
| 2007-12-06 |
cjfields | small fix for VERSIONing issue, POD fixes
|
commit | commitdiff | tree |
| 2007-11-29 |
cjfields | bug 2333; first pass at PSIBLAST XML parsing
|
commit | commitdiff | tree |
| 2007-11-29 |
cjfields | Match HSP, not hit table
|
commit | commitdiff | tree |
| 2007-11-29 |
cjfields | more memory-friendly
|
commit | commitdiff | tree |
| 2007-11-28 |
cjfields | WUBLAST signif gets pvalue, NCBI BLAST signif gets...
|
commit | commitdiff | tree |
| 2007-11-28 |
cjfields | Several fixes
|
commit | commitdiff | tree |
| 2007-11-25 |
cjfields | bug 2329
|
commit | commitdiff | tree |
| 2007-11-25 |
cjfields | bug 2329, example script to generate a SVG chromatogram
|
commit | commitdiff | tree |
| 2007-11-25 |
cjfields | bug 2329
|
commit | commitdiff | tree |
| 2007-11-25 |
cjfields | get rid of 'Use of uninitialized value in concatenation...
|
commit | commitdiff | tree |
| 2007-11-25 |
cjfields | Related to Albert's fix
|
commit | commitdiff | tree |
| 2007-11-21 |
cjfields | bug 2399
|
commit | commitdiff | tree |
| 2007-11-21 |
cjfields | a bit more for bug 2391
|
commit | commitdiff | tree |
| 2007-11-21 |
cjfields | bug 2391
|
commit | commitdiff | tree |
| 2007-11-21 |
cjfields | bug 2406
|
commit | commitdiff | tree |
| 2007-11-19 |
cjfields | bug 2392
|
commit | commitdiff | tree |
| 2007-11-19 |
cjfields | bug 2399
|
commit | commitdiff | tree |
| 2007-11-16 |
cjfields | fix fuzzy location bug
|
commit | commitdiff | tree |
| 2007-11-13 |
cjfields | Now catches primary GI
|
commit | commitdiff | tree |
| 2007-11-10 |
cjfields | Fix for mysql adaptor to recursively remove child features...
|
commit | commitdiff | tree |
| 2007-11-08 |
cjfields | fix arg list not being passed along if GFF3 is intended
|
commit | commitdiff | tree |
| 2007-11-08 |
cjfields | Allow phase to be set
|
commit | commitdiff | tree |
| 2007-11-08 |
cjfields | * alias delete_features (for GBrowse plugins)
|
commit | commitdiff | tree |
| 2007-10-23 |
cjfields | error in test script
|
commit | commitdiff | tree |
| 2007-10-23 |
cjfields | bug 2385
|
commit | commitdiff | tree |
| 2007-10-23 |
cjfields | bug 2368
|
commit | commitdiff | tree |
| 2007-10-23 |
cjfields | bug 2367
|
commit | commitdiff | tree |
| 2007-10-18 |
cjfields | some tweaks
|
commit | commitdiff | tree |
| 2007-10-15 |
cjfields | bug 2332
|
commit | commitdiff | tree |
| 2007-10-09 |
cjfields | start must always be < end; strand determines directionality
|
commit | commitdiff | tree |
| 2007-10-08 |
cjfields | capture display_name, score data for Glimmer3 predict...
|
commit | commitdiff | tree |
| 2007-10-05 |
cjfields | typo
|
commit | commitdiff | tree |
| 2007-10-05 |
cjfields | * bug fix from Jeffrey Barrick for cases where empty...
|
commit | commitdiff | tree |
| 2007-10-04 |
cjfields | always use table type to MyISAM for FULLTEXT indexing
|
commit | commitdiff | tree |
| 2007-09-28 |
cjfields | don't use Carp, use $self->warn()
|
commit | commitdiff | tree |
| 2007-09-28 |
cjfields | fix bug with multiple ID, DE, AC lines
|
commit | commitdiff | tree |
| 2007-09-27 |
cjfields | * add line_length parameter for stockholm to print...
|
commit | commitdiff | tree |
| 2007-09-27 |
cjfields | Add meta data to alignments if present
|
commit | commitdiff | tree |
| 2007-09-27 |
cjfields | remove nonexistent exported sub
|
commit | commitdiff | tree |
| 2007-09-27 |
cjfields | minor change to prevent scripts from dying
|
commit | commitdiff | tree |
| 2007-09-27 |
cjfields | Add obo to registry
|
commit | commitdiff | tree |
| 2007-09-27 |
cjfields | Switch to using SO and OBO
|
commit | commitdiff | tree |
| 2007-09-25 |
cjfields | Rollback last commit, don't want to change lca node...
|
commit | commitdiff | tree |
| 2007-09-25 |
cjfields | bug 2219
|
commit | commitdiff | tree |
| 2007-09-24 |
cjfields | POD fix
|
commit | commitdiff | tree |
| 2007-09-17 |
cjfields | remove overloading exceptions (more trouble than they...
|
commit | commitdiff | tree |
| 2007-09-14 |
cjfields | mail list patch from Jay Hannah
|
commit | commitdiff | tree |
| 2007-09-14 |
cjfields | bug 2352
|
commit | commitdiff | tree |
| 2007-09-11 |
cjfields | bug 2358
|
commit | commitdiff | tree |
| 2007-09-10 |
cjfields | bug 2350
|
commit | commitdiff | tree |
| 2007-09-10 |
cjfields | bug 2354
|
commit | commitdiff | tree |
| 2007-09-10 |
cjfields | bug 2358, added some more tests for Assembly objects
|
commit | commitdiff | tree |
| 2007-09-08 |
cjfields | bug 2358
|
commit | commitdiff | tree |
| 2007-09-05 |
cjfields | Shouldn't use Carp, use throw/warn instead
|
commit | commitdiff | tree |
| 2007-09-05 |
cjfields | 2357
|
commit | commitdiff | tree |
| 2007-09-05 |
cjfields | add in hack for alignment viewer
|
commit | commitdiff | tree |
| 2007-09-05 |
cjfields | change sub redefining to to simple handler dispatch
|
commit | commitdiff | tree |
