| 51b990d | Eddie Belter | 07 March 2013, 22:37:06 UTC | MC16s: get assembler params inline while processing sanger inst data | 07 March 2013, 22:37:06 UTC |
| e192dd0 | Eddie Belter | 07 March 2013, 22:23:56 UTC | MC16s: remove unused prepare inst data method | 07 March 2013, 22:23:56 UTC |
| 447ed58 | Scott Smith | 07 March 2013, 21:38:13 UTC | updated clinseq convergeSnvs.t and convergeIndels.t to use new data, and a copy of the original test models which will not change | 07 March 2013, 21:38:13 UTC |
| 638fc22 | Scott Smith | 07 March 2013, 21:30:19 UTC | make Genome::Command::WithSavedResults abstract, and check for implementation of result_verison at subclass declaration time (make this abstract too eventually) | 07 March 2013, 21:30:19 UTC |
| aa505a8 | Scott Smith | 07 March 2013, 21:28:41 UTC | fix engrish | 07 March 2013, 21:28:41 UTC |
| 68ad9a6 | Scott Smith | 07 March 2013, 21:25:56 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 07 March 2013, 21:25:56 UTC |
| 08b903d | Thomas Mooney | 07 March 2013, 20:37:25 UTC | Diffed due to annotation bugfixes. Update blessed somvar build. | 07 March 2013, 20:37:25 UTC |
| 35f23df | Eddie Belter | 07 March 2013, 20:15:56 UTC | MC16s: update blessed 454 build | 07 March 2013, 20:15:56 UTC |
| dcd50ee | Eddie Belter | 07 March 2013, 20:14:44 UTC | MC16s: rm events! This model is officially work flowified! | 07 March 2013, 20:14:58 UTC |
| d5b0e32 | Eddie Belter | 06 March 2013, 23:45:13 UTC | MC16s: reports command for workflow | 07 March 2013, 20:14:58 UTC |
| 35a81b1 | Eddie Belter | 06 March 2013, 23:39:34 UTC | MC16s: made merge sx results work | 07 March 2013, 20:14:57 UTC |
| 14b2907 | Eddie Belter | 06 March 2013, 23:38:57 UTC | MC16s: complete workflow | 07 March 2013, 20:14:57 UTC |
| 16af912 | Eddie Belter | 06 March 2013, 01:10:06 UTC | MC16s: add workflow to model | 07 March 2013, 20:14:56 UTC |
| 43867bc | Eddie Belter | 06 March 2013, 00:52:02 UTC | MC16s: rm build sub class method that was not used | 07 March 2013, 20:14:56 UTC |
| ac6eea4 | Eddie Belter | 06 March 2013, 00:49:39 UTC | MC16s: add classifier validation; use classifier in build | 07 March 2013, 20:14:55 UTC |
| affa958 | Eddie Belter | 06 March 2013, 00:43:04 UTC | MC16s: move pp params to model | 07 March 2013, 20:14:55 UTC |
| f29697c | Mark Burnett | 07 March 2013, 19:58:35 UTC | whitespace and sorting | 07 March 2013, 19:58:35 UTC |
| 82f82b7 | Mark Burnett | 07 March 2013, 19:55:22 UTC | add snap model file abbreviations (RT #90847) | 07 March 2013, 19:55:22 UTC |
| 1d49e00 | Scott Smith | 07 March 2013, 03:33:31 UTC | give software results a better display name | 07 March 2013, 03:33:31 UTC |
| 188a5c3 | Scott Smith | 07 March 2013, 03:32:09 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 07 March 2013, 03:32:09 UTC |
| ac52703 | Scott Smith | 07 March 2013, 03:32:05 UTC | updated converge tests to new test models | 07 March 2013, 03:32:05 UTC |
| 184a2ec | Scott Smith | 07 March 2013, 03:31:32 UTC | switch test model: previous one was deleted today | 07 March 2013, 03:31:32 UTC |
| 5f2e5ba | Malachi Griffith | 07 March 2013, 03:18:22 UTC | ClinSeq - completed first version of clin-seq converge all-events with visualizations and associated unit test | 07 March 2013, 03:18:22 UTC |
| 2d3ba7a | Gabriel Sanderson | 06 March 2013, 23:35:21 UTC | Merge branch 'master' into gb_master | 06 March 2013, 23:35:21 UTC |
| 48ea23c | Gabriel Sanderson | 06 March 2013, 23:34:51 UTC | Make the "fake_parent" match more flexible so we can have multiple fake_parent samples | 06 March 2013, 23:35:01 UTC |
| 321cca1 | Scott Smith | 06 March 2013, 23:23:56 UTC | Merge branch 'master' of github.com:genome/gms-core | 06 March 2013, 23:23:56 UTC |
| ba36b0d | Scott Smith | 06 March 2013, 23:21:28 UTC | fix typo in GENOME_TEST_URL.pm module | 06 March 2013, 23:21:28 UTC |
| 85f8929 | Malachi Griffith | 06 March 2013, 21:43:56 UTC | ClinSeq - first version of R code to create all events heatmap | 06 March 2013, 21:43:56 UTC |
| d795181 | Malachi Griffith | 06 March 2013, 21:42:52 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 March 2013, 21:42:52 UTC |
| 2e5b741 | nnutter | 06 March 2013, 21:03:03 UTC | fix bug in print_message | 06 March 2013, 21:03:03 UTC |
| 7872dfd | APipe Tester | 06 March 2013, 20:49:00 UTC | updated workflow submodule to d356e72 | 06 March 2013, 20:49:00 UTC |
| bbf216b | APipe Tester | 06 March 2013, 20:36:40 UTC | updated workflow submodule to 3bb598b | 06 March 2013, 20:36:40 UTC |
| 953e4ae | Scott Smith | 06 March 2013, 19:40:23 UTC | remove debug message from rnaseq | 06 March 2013, 19:40:23 UTC |
| 9699146 | Scott Smith | 06 March 2013, 19:39:07 UTC | test case for RnaSeq strategy processing | 06 March 2013, 19:39:07 UTC |
| 93f640e | Scott Smith | 06 March 2013, 19:31:51 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 March 2013, 19:31:51 UTC |
| 2e0d02d | Scott Smith | 06 March 2013, 19:31:43 UTC | update default software result generation to not stomp on the output dir | 06 March 2013, 19:31:43 UTC |
| 9797b4d | APipe Tester | 06 March 2013, 18:57:01 UTC | Updated `gmt` tab completion. | 06 March 2013, 18:57:01 UTC |
| 2063136 | APipe Tester | 06 March 2013, 18:55:52 UTC | Updated `genome` tab completion. | 06 March 2013, 18:55:52 UTC |
| 71810ce | APipe Tester | 06 March 2013, 18:10:15 UTC | Updated `gmt` tab completion. | 06 March 2013, 18:10:17 UTC |
| 937199e | APipe Tester | 06 March 2013, 18:09:12 UTC | Updated `genome` tab completion. | 06 March 2013, 18:10:17 UTC |
| a2666d3 | Scott Smith | 06 March 2013, 16:59:38 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 March 2013, 16:59:38 UTC |
| 107ba57 | Scott Smith | 06 March 2013, 16:59:24 UTC | remove DB::single | 06 March 2013, 16:59:24 UTC |
| 9cff663 | Jason Walker | 06 March 2013, 16:58:10 UTC | Add new input parameters to match picard 1.82. | 06 March 2013, 16:58:10 UTC |
| ae5deb1 | Scott Smith | 06 March 2013, 16:58:05 UTC | updated rnaseq align-reads to present underlying individual alignment results as outputs | 06 March 2013, 16:58:05 UTC |
| dbbb161 | Scott Smith | 06 March 2013, 16:43:19 UTC | Added digital_expression_detection_strategy to RNASeq. Not fully functional yet. | 06 March 2013, 16:43:19 UTC |
| 98fec5c | kmeltzst | 06 March 2013, 15:10:06 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 March 2013, 15:10:06 UTC |
| 41ca7bd | Scott Smith | 06 March 2013, 04:51:50 UTC | updated "gmt htseq" and related infrastructure | 06 March 2013, 04:51:50 UTC |
| a7efb91 | Scott Smith | 06 March 2013, 04:50:43 UTC | fix to work with non-deprecated models | 06 March 2013, 04:50:43 UTC |
| b98bbee | Scott Smith | 06 March 2013, 04:47:50 UTC | updated converge{Svs,Indels,Cnvs,Stats}.t | 06 March 2013, 04:47:50 UTC |
| 6981130 | Scott Smith | 06 March 2013, 04:42:21 UTC | updated convergeSnvs.t for changed data | 06 March 2013, 04:42:21 UTC |
| 1fee2ac | Malachi Griffith | 06 March 2013, 04:22:28 UTC | ClinSeq - first complete version of converge all-events | 06 March 2013, 04:22:28 UTC |
| e7841aa | Malachi Griffith | 06 March 2013, 00:06:59 UTC | ClinSeq fix workflow | 06 March 2013, 00:06:59 UTC |
| 838979b | Malachi Griffith | 06 March 2013, 00:06:09 UTC | Htseq - Add to rna extraction types recognized by regex | 06 March 2013, 00:06:09 UTC |
| 5035637 | Malachi Griffith | 06 March 2013, 00:05:07 UTC | Blessing new clinseq build | 06 March 2013, 00:05:07 UTC |
| fd8f52a | Eddie Belter | 05 March 2013, 23:05:44 UTC | Sync: uncommented out a needed method. This was accidentally committed | 05 March 2013, 23:06:11 UTC |
| 82756ad | apregier | 05 March 2013, 22:32:02 UTC | Merge branch 'fireteam2' into gb_master | 05 March 2013, 22:32:02 UTC |
| d76c7f4 | apregier | 05 March 2013, 22:26:21 UTC | In the case where the variant falls in a degenerate codon, the mutation should be labeled silent | 05 March 2013, 22:26:21 UTC |
| 5ce5114 | apregier | 05 March 2013, 21:06:00 UTC | Merge branch 'fireteam2' into gb_master | 05 March 2013, 21:06:00 UTC |
| 796d443 | apregier | 05 March 2013, 20:58:47 UTC | Create derivatives of gtf file for rna-seq-only imported annotation build | 05 March 2013, 20:58:47 UTC |
| d99b702 | Dan Koboldt | 05 March 2013, 20:51:23 UTC | Correction to apparent default setting | 05 March 2013, 20:51:23 UTC |
| 63fe2de | Dan Koboldt | 05 March 2013, 20:50:00 UTC | Corrected a bug. Merge branch 'master' of git+ssh://git/srv/git/genome | 05 March 2013, 20:50:00 UTC |
| 0e67c4a | Dan Koboldt | 05 March 2013, 20:49:49 UTC | Correction to small bug that was causing all gene exons to be printed | 05 March 2013, 20:49:49 UTC |
| b041a07 | Eddie Belter | 05 March 2013, 19:19:03 UTC | MC16s: use default pp id method to get pp in run status command | 05 March 2013, 19:19:03 UTC |
| cfb68e1 | Eddie Belter | 05 March 2013, 18:58:22 UTC | Sync: fail if getting current value encounters error; add msg checks to tests | 05 March 2013, 18:58:30 UTC |
| 74b872c | apregier | 05 March 2013, 18:44:45 UTC | Merge branch 'fireteam2' into gb_master | 05 March 2013, 18:44:45 UTC |
| 2e23edf | apregier | 05 March 2013, 18:43:35 UTC | Remove non-temp file path | 05 March 2013, 18:43:44 UTC |
| 91b4bee | Scott Smith | 05 March 2013, 18:42:18 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: .gitmodules | 05 March 2013, 18:42:18 UTC |
| fa59da3 | Scott Smith | 05 March 2013, 18:40:19 UTC | add vendor/rna-star -currently empty, testing in-progress | 05 March 2013, 18:40:19 UTC |
| e0606f7 | Eddie Belter | 05 March 2013, 16:50:31 UTC | Sync: get current value before checking if property is updated | 05 March 2013, 16:50:31 UTC |
| 12b8489 | Eddie Belter | 05 March 2013, 16:45:57 UTC | Sync: attempt to update genome entity directly first, then via attrs in base for attrs | 05 March 2013, 16:46:03 UTC |
| 571be86 | apregier | 05 March 2013, 16:45:06 UTC | Merge branch 'fireteam2' into gb_master | 05 March 2013, 16:45:06 UTC |
| fb548b9 | apregier | 05 March 2013, 16:44:25 UTC | Skipped updates do not have errors | 05 March 2013, 16:44:36 UTC |
| 42f7e41 | apregier | 05 March 2013, 16:29:46 UTC | Check for properties that are not via attributes and send them to the parent method. | 05 March 2013, 16:44:36 UTC |
| fe29fbc | apregier | 05 March 2013, 03:36:55 UTC | Reenable annotator version 3 tests | 05 March 2013, 16:44:35 UTC |
| 88eb4a1 | apregier | 05 March 2013, 03:36:19 UTC | Fix bugs in annotator | 05 March 2013, 16:44:35 UTC |
| 66ae53c | apregier | 05 March 2013, 03:33:37 UTC | Fix bug in codons_in_range when the exon is very short | 05 March 2013, 16:44:35 UTC |
| 9e0338e | apregier | 05 March 2013, 03:32:49 UTC | Fix warning due to some abandoned builds not having versions | 05 March 2013, 16:44:34 UTC |
| 8846058 | Ling Lin | 05 March 2013, 16:40:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome just wish to merge as prompted. | 05 March 2013, 16:40:10 UTC |
| 3a84113 | kmeltzst | 05 March 2013, 14:57:41 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 March 2013, 14:57:41 UTC |
| 2fddde5 | APipe Tester | 04 March 2013, 23:03:34 UTC | updated jenkins submodule to 5f3f651 | 04 March 2013, 23:03:34 UTC |
| 569fdcf | APipe Tester | 04 March 2013, 23:01:12 UTC | updated gms-config submodule to 6ccaa62 | 04 March 2013, 23:01:12 UTC |
| 49259e6 | APipe Tester | 04 March 2013, 22:57:14 UTC | updated gms-config submodule to f4f7915 | 04 March 2013, 22:57:14 UTC |
| c185b2c | APipe Tester | 04 March 2013, 22:50:44 UTC | updated gms-config submodule to 96f904a | 04 March 2013, 22:50:44 UTC |
| 8839798 | Ben Oberkfell | 04 March 2013, 22:47:57 UTC | commit is controlled by the parent process. override commit locally to be a no-op so we do not double commit. | 04 March 2013, 22:47:57 UTC |
| 46cfa59 | Nathan Nutter | 04 March 2013, 21:32:07 UTC | trying to fix compile error and test failures | 04 March 2013, 21:32:27 UTC |
| 74433ec | Malachi Griffith | 04 March 2013, 21:26:34 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2013, 21:26:34 UTC |
| 5981d17 | Malachi Griffith | 04 March 2013, 21:26:20 UTC | ClinSeq - Fix missing dirs error for variant sources step | 04 March 2013, 21:26:20 UTC |
| dd34e88 | APipe Tester | 04 March 2013, 21:17:10 UTC | updated configuration-manager submodule to f719544 | 04 March 2013, 21:17:10 UTC |
| 0c03be0 | APipe Tester | 04 March 2013, 21:05:23 UTC | updated configuration-manager submodule to 93070ad | 04 March 2013, 21:05:23 UTC |
| 054eeac | Adam Coffman | 04 March 2013, 20:54:24 UTC | add configuration related submodules | 04 March 2013, 20:58:26 UTC |
| 3e75614 | Adam Coffman | 04 March 2013, 20:44:42 UTC | add config manager and config directory submodules | 04 March 2013, 20:58:25 UTC |
| 3db2f92 | APipe Tester | 04 March 2013, 20:51:09 UTC | updated workflow submodule to 9f9f689 | 04 March 2013, 20:51:09 UTC |
| 00a452d | Eddie Belter | 04 March 2013, 17:55:05 UTC | Sync: syntax err in index illumina sql | 04 March 2013, 17:55:05 UTC |
| ebe22be | Eddie Belter | 04 March 2013, 17:53:44 UTC | Sync: update ri454 test output | 04 March 2013, 17:53:51 UTC |
| 2dfce1f | kmeltzst | 04 March 2013, 17:45:39 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2013, 17:45:39 UTC |
| a192752 | kmeltzst | 04 March 2013, 17:42:19 UTC | allow for empty output files | 04 March 2013, 17:42:19 UTC |
| 41b15f3 | Scott Smith | 04 March 2013, 17:34:31 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2013, 17:34:31 UTC |
| 0d4498b | Scott Smith | 04 March 2013, 17:34:22 UTC | add vendor/htseq | 04 March 2013, 17:34:22 UTC |
| 371679e | Eddie Belter | 28 February 2013, 21:25:03 UTC | Sync: consolidate and add tests for ii | 04 March 2013, 17:32:00 UTC |
| 970ef39 | Eddie Belter | 28 February 2013, 21:24:28 UTC | Sync: try to get current value as direct property from genome entity | 04 March 2013, 17:32:00 UTC |
