| ee6a7cd | Jasreet Hundal | 16 July 2013, 19:15:26 UTC | Output Cds sequence for annotated snv file | 16 July 2013, 19:15:26 UTC |
| f40a60a | APipe Tester | 16 July 2013, 18:24:27 UTC | updated ur submodule to fc39b18 | 16 July 2013, 18:24:27 UTC |
| 58e488f | Ian Ferguson | 16 July 2013, 17:54:46 UTC | Bwamem now closes db handle during align and sort | 16 July 2013, 17:55:31 UTC |
| b75157b | Nathan Nutter | 16 July 2013, 17:26:23 UTC | Sort::strverscmp is now packaged | 16 July 2013, 17:26:36 UTC |
| 16a0f0c | APipe Tester | 16 July 2013, 15:36:20 UTC | updated ur submodule to e8a55d2 | 16 July 2013, 15:36:20 UTC |
| e72b646 | Thomas Mooney | 16 July 2013, 15:05:32 UTC | Make sure $@ doesn't get swallowed before we print our error. | 16 July 2013, 15:05:32 UTC |
| 692e155 | Ben Oberkfell | 15 July 2013, 22:14:00 UTC | Revert "pass the "force" param forward when copying models." This reverts commit ff03c8c755e7c34fc801cbc538f0cea133185c1e. | 15 July 2013, 22:14:00 UTC |
| 7af270b | Ben Oberkfell | 15 July 2013, 21:49:43 UTC | do not attempt to call properties where the model class does not define it | 15 July 2013, 21:49:43 UTC |
| ff03c8c | Ben Oberkfell | 15 July 2013, 21:22:51 UTC | pass the "force" param forward when copying models. | 15 July 2013, 21:22:51 UTC |
| 0ae1e9b | Chris Miller | 15 July 2013, 17:08:02 UTC | updating help | 15 July 2013, 17:21:41 UTC |
| a5b3daa | APipe Tester | 15 July 2013, 16:36:31 UTC | Updated `gmt` tab completion. | 15 July 2013, 16:36:50 UTC |
| 126a199 | APipe Tester | 15 July 2013, 16:34:37 UTC | Updated `genome` tab completion. | 15 July 2013, 16:36:50 UTC |
| 396bed1 | APipe Tester | 15 July 2013, 16:30:49 UTC | Updated class browser cache. | 15 July 2013, 16:36:49 UTC |
| 62c97f5 | Scott Smith | 15 July 2013, 16:30:30 UTC | fixed clinseq TestGenomeCommands for new input data | 15 July 2013, 16:30:30 UTC |
| 33bcbb6 | Scott Smith | 15 July 2013, 16:24:42 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 July 2013, 16:24:42 UTC |
| 1623f11 | Scott Smith | 15 July 2013, 16:24:32 UTC | updated clinseq convergeStats.t to use new output with different sorting | 15 July 2013, 16:24:32 UTC |
| 2448659 | Travis Abbott | 15 July 2013, 16:17:12 UTC | add breakdancer 1.4.2 | 15 July 2013, 16:17:12 UTC |
| b1ef0c7 | APipe Tester | 15 July 2013, 15:50:58 UTC | Updated `gmt` tab completion. | 15 July 2013, 15:50:58 UTC |
| b00b304 | APipe Tester | 15 July 2013, 15:49:45 UTC | Updated `genome` tab completion. | 15 July 2013, 15:49:45 UTC |
| da78f7e | APipe Tester | 15 July 2013, 15:47:23 UTC | Updated class browser cache. | 15 July 2013, 15:47:23 UTC |
| 977ff34 | Chris Miller | 15 July 2013, 15:37:29 UTC | adding option for max clusters | 15 July 2013, 15:37:59 UTC |
| 2c19cbd | APipe Tester | 12 July 2013, 21:09:56 UTC | Updated `genome` tab completion. | 12 July 2013, 21:09:56 UTC |
| 5a5f456 | APipe Tester | 12 July 2013, 21:08:21 UTC | Updated class browser cache. | 12 July 2013, 21:08:21 UTC |
| 85b97ea | Malachi Griffith | 12 July 2013, 20:42:59 UTC | Clinseq - fix create-mutation-diagrams test to ingore fields contain floating point values and update test result to account for update to cosmic v65 | 12 July 2013, 20:42:59 UTC |
| ba7dd28 | APipe Tester | 12 July 2013, 19:46:16 UTC | updated workflow submodule to 7bf85e2 | 12 July 2013, 19:46:16 UTC |
| a85f660 | Nathan Nutter | 12 July 2013, 15:13:55 UTC | more aggressive abandoning of unstartable builds Change behavior so that it abandons Unstartable builds as soon as long as the latest_build was not Unstartable. This should lower "double counting" builds that have failures and unstartables. | 12 July 2013, 19:26:43 UTC |
| e867197 | dmorton | 11 July 2013, 17:04:02 UTC | extracted methods in Genome::Model::Build::all_allocations | 12 July 2013, 16:27:37 UTC |
| 3baaece | dmorton | 10 July 2013, 18:56:08 UTC | Created 'genome instrument-data find-associated-builds' | 12 July 2013, 16:27:37 UTC |
| d0bf02a | dmorton | 10 July 2013, 18:41:43 UTC | Fix error getting eaten in build.pm | 12 July 2013, 16:27:37 UTC |
| d6cd4fa | APipe Tester | 12 July 2013, 13:37:39 UTC | updated workflow submodule to 81c111c | 12 July 2013, 13:37:39 UTC |
| c7aa9bf | APipe Tester | 12 July 2013, 03:58:52 UTC | updated workflow submodule to 1985352 | 12 July 2013, 03:58:52 UTC |
| f5845c6 | Malachi Griffith | 12 July 2013, 02:47:03 UTC | Update test data to accomodate updates to clin-seq update-analysis | 12 July 2013, 02:47:03 UTC |
| 13f1bd7 | Malachi Griffith | 12 July 2013, 02:10:35 UTC | Updated doc for clin-seq | 12 July 2013, 02:10:35 UTC |
| 9ce5304 | Malachi Griffith | 12 July 2013, 01:58:23 UTC | ClinSeq - add logic to improve handling of data additions | 12 July 2013, 01:58:23 UTC |
| 584a9c8 | Malachi Griffith | 11 July 2013, 22:53:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 11 July 2013, 22:53:03 UTC |
| 5eaeb43 | Malachi Griffith | 11 July 2013, 22:52:50 UTC | ClinSeq - Update test result for UpdateAnalysis | 11 July 2013, 22:52:50 UTC |
| 7e56672 | Scott Smith | 11 July 2013, 22:42:04 UTC | disabled test until test model completes building | 11 July 2013, 22:42:04 UTC |
| 2c8903b | Malachi Griffith | 11 July 2013, 21:51:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 11 July 2013, 21:51:54 UTC |
| 4662490 | Malachi Griffith | 11 July 2013, 21:51:44 UTC | Fix typo in clinseq annotation database variable name | 11 July 2013, 21:51:44 UTC |
| 27a3f5e | Scott Smith | 11 July 2013, 21:25:48 UTC | updated to match meta-data changes on samples | 11 July 2013, 21:25:48 UTC |
| dfa5703 | Scott Smith | 11 July 2013, 21:22:07 UTC | update clinseq tests due to changing underlying data | 11 July 2013, 21:22:07 UTC |
| d1ed931 | Scott Smith | 11 July 2013, 21:04:18 UTC | readme on constructing cancer annotation for clinseq | 11 July 2013, 21:04:18 UTC |
| 6c0746a | Scott Smith | 11 July 2013, 19:29:05 UTC | updated clinseq to use Genome::Db::Cosmic directly instead of the legacy files under the cancer annotation db. | 11 July 2013, 19:29:05 UTC |
| 2f1eb22 | apregier | 11 July 2013, 18:44:58 UTC | Merge branch 'annovar' into gb_master | 11 July 2013, 18:44:58 UTC |
| c70a49e | apregier | 11 July 2013, 17:57:49 UTC | Include rsid in maf output | 11 July 2013, 18:18:25 UTC |
| 69fa554 | apregier | 11 July 2013, 17:26:35 UTC | Include regdb score in annot file | 11 July 2013, 18:18:25 UTC |
| 65b6e19 | apregier | 12 June 2013, 21:00:25 UTC | Annotate tier1 with regulatory variants as well | 11 July 2013, 18:18:24 UTC |
| a209db0 | APipe Tester | 11 July 2013, 17:16:28 UTC | Updated `gmt` tab completion. | 11 July 2013, 17:16:39 UTC |
| 30b877a | APipe Tester | 11 July 2013, 17:15:38 UTC | Updated `genome` tab completion. | 11 July 2013, 17:16:39 UTC |
| 0c72cf4 | APipe Tester | 11 July 2013, 17:13:57 UTC | Updated class browser cache. | 11 July 2013, 17:16:39 UTC |
| 1a77f24 | Jason Walker | 11 July 2013, 17:15:24 UTC | Add a basic test for Sword SlidingWindowPileup | 11 July 2013, 17:15:24 UTC |
| 103716b | Jason Walker | 11 July 2013, 17:06:06 UTC | Add a new tree to genome model tools for Sword development | 11 July 2013, 17:06:06 UTC |
| 729ceef | APipe Tester | 11 July 2013, 14:14:22 UTC | updated workflow submodule to f58f5eb | 11 July 2013, 14:14:22 UTC |
| 9db1415 | Nathan Nutter | 11 July 2013, 06:28:29 UTC | rewrite strverscmp because the old one was broken | 11 July 2013, 06:28:29 UTC |
| 58b19de | APipe Tester | 11 July 2013, 03:19:13 UTC | Updated `gmt` tab completion. | 11 July 2013, 03:19:13 UTC |
| 35d8250 | APipe Tester | 11 July 2013, 03:18:13 UTC | Updated `genome` tab completion. | 11 July 2013, 03:18:13 UTC |
| 9a5936e | APipe Tester | 11 July 2013, 03:15:42 UTC | Updated class browser cache. | 11 July 2013, 03:15:42 UTC |
| 5778b7f | Dave Larson | 11 July 2013, 03:02:09 UTC | Query out the library name for BamQC summarization. | 11 July 2013, 03:02:09 UTC |
| 72bd7fe | Chris Miller | 11 July 2013, 00:22:19 UTC | fixing bed conversion issue | 11 July 2013, 00:22:58 UTC |
| 3c1032c | Scott Smith | 11 July 2013, 00:14:57 UTC | switch to specific subclasses of Genome::Db for clinseq inputs | 11 July 2013, 00:15:09 UTC |
| efc8d54 | Gabriel Sanderson | 10 July 2013, 22:37:58 UTC | Merge branch 'master' into gb_master | 10 July 2013, 22:37:58 UTC |
| bf36cd9 | Gabriel Sanderson | 10 July 2013, 22:37:43 UTC | Since this test uses shellcmd (and should not)... force a use of the module that is being tested so that test tracker can catch failures easier. | 10 July 2013, 22:37:43 UTC |
| a94b24d | Gabriel Sanderson | 10 July 2013, 22:32:07 UTC | Merge branch 'master' into gb_master | 10 July 2013, 22:32:07 UTC |
| 4e821ba | Gabriel Sanderson | 10 July 2013, 22:28:01 UTC | Updated test for new required property | 10 July 2013, 22:30:56 UTC |
| 283cf91 | Feiyu Du | 10 July 2013, 21:41:46 UTC | skip bamqc for imported alignment bam | 10 July 2013, 21:41:46 UTC |
| 1612f25 | Scott Smith | 10 July 2013, 21:22:11 UTC | No longer require a .git subdirectory in a Genome::Db dir, or a "latest" symlink. A meta.yml file is sufficient. | 10 July 2013, 21:22:43 UTC |
| 7a0d6cc | APipe Tester | 10 July 2013, 20:46:53 UTC | Updated `gmt` tab completion. | 10 July 2013, 20:46:53 UTC |
| dd860d9 | APipe Tester | 10 July 2013, 20:45:58 UTC | Updated `genome` tab completion. | 10 July 2013, 20:45:58 UTC |
| f38f394 | APipe Tester | 10 July 2013, 20:43:48 UTC | Updated class browser cache. | 10 July 2013, 20:43:48 UTC |
| b248d55 | Scott Smith | 10 July 2013, 20:31:43 UTC | updated the blessed-build for clinseq: the diff changes when LIMS archives data, and this just occurred | 10 July 2013, 20:32:08 UTC |
| 808c854 | Scott Smith | 10 July 2013, 20:27:51 UTC | ensure that we only fabricate subclasses for things that inherit from Genome::Db | 10 July 2013, 20:32:08 UTC |
| e819329 | Scott Smith | 10 July 2013, 20:24:39 UTC | merge error fix in Genome::Db | 10 July 2013, 20:32:07 UTC |
| a7a889e | APipe Tester | 10 July 2013, 20:25:19 UTC | Updated `gmt` tab completion. | 10 July 2013, 20:25:19 UTC |
| 666055b | APipe Tester | 10 July 2013, 20:24:15 UTC | Updated `genome` tab completion. | 10 July 2013, 20:24:15 UTC |
| 6e30a5b | APipe Tester | 10 July 2013, 20:22:13 UTC | Updated class browser cache. | 10 July 2013, 20:22:13 UTC |
| 64c6193 | Scott Smith | 10 July 2013, 20:15:13 UTC | updated the clinseq pipeline to use Genome::Db entities instead of a hard-coded path to special annotation data | 10 July 2013, 20:15:13 UTC |
| 874aa4d | Scott Smith | 10 July 2013, 20:08:13 UTC | updated to sub-class by source and database | 10 July 2013, 20:08:50 UTC |
| e892650 | APipe Tester | 10 July 2013, 18:54:59 UTC | Updated `gmt` tab completion. | 10 July 2013, 18:54:59 UTC |
| d0c8d53 | APipe Tester | 10 July 2013, 18:53:45 UTC | Updated `genome` tab completion. | 10 July 2013, 18:53:45 UTC |
| 8bbb3b8 | APipe Tester | 10 July 2013, 18:51:33 UTC | Updated class browser cache. | 10 July 2013, 18:51:33 UTC |
| 1eb8bf5 | Feiyu Du | 10 July 2013, 18:26:26 UTC | bug fix | 10 July 2013, 18:26:26 UTC |
| f84b75c | Jason Walker | 10 July 2013, 17:21:46 UTC | Merge t push branch 'master' of ssh://git/srv/git/genome | 10 July 2013, 17:21:46 UTC |
| 8666282 | Jason Walker | 10 July 2013, 17:21:37 UTC | Add PCT_CHIMERAS to the BamQcMetrics summary per refalign build. | 10 July 2013, 17:21:37 UTC |
| eb01eb0 | Dave Larson | 10 July 2013, 03:04:16 UTC | Change workflow command construction to use ref($self) instead of __PACKAGE__ so inheritance does what we want. | 10 July 2013, 03:04:16 UTC |
| 4ee0e24 | APipe Tester | 09 July 2013, 22:07:12 UTC | updated ur submodule to bfb9399 | 09 July 2013, 22:07:12 UTC |
| 93e955a | Chris Miller | 09 July 2013, 21:38:21 UTC | removing depricated tool | 09 July 2013, 21:38:21 UTC |
| 5840552 | Eddie Belter | 09 July 2013, 21:05:07 UTC | SomVal: identify dnp result uses bam_path to get bam from aligned bam result | 09 July 2013, 21:05:07 UTC |
| 2c8f46c | Thomas Mooney | 09 July 2013, 20:47:53 UTC | Don't try to run coverage analysis without an ROI. | 09 July 2013, 20:47:53 UTC |
| 63f4c69 | Thomas Mooney | 09 July 2013, 20:47:13 UTC | Only restrict to target regions if we have an ROI. | 09 July 2013, 20:47:13 UTC |
| ecc6fef | Thomas Mooney | 09 July 2013, 20:46:39 UTC | Change to parent class so we can operate on refined BAMs. | 09 July 2013, 20:46:39 UTC |
| 98c0ac8 | Jason Walker | 09 July 2013, 18:03:37 UTC | A new command line tool to summarize BamQc metrics per build by instrument data. | 09 July 2013, 18:03:37 UTC |
| 6982200 | Eddie Belter | 08 July 2013, 23:00:09 UTC | InstData GATK: base recalibrator uses allocation tmp dir for gatk print reads | 09 July 2013, 17:26:03 UTC |
| c4dfa2f | Eddie Belter | 08 July 2013, 22:51:08 UTC | GMT GATK: add tmp dir option | 09 July 2013, 17:26:03 UTC |
| 9d3f59f | Eddie Belter | 08 July 2013, 21:39:36 UTC | Inst Data Refine Reads Gatk: use indel realigner as bam, source for base recalibrator | 09 July 2013, 17:26:03 UTC |
| 8a0aece | Eddie Belter | 08 July 2013, 20:33:14 UTC | InstData Aligned Bam: add bam_file alias | 09 July 2013, 17:26:02 UTC |
| cdf746e | Eddie Belter | 08 July 2013, 20:27:33 UTC | InstData GATK: add inst data property to base | 09 July 2013, 17:26:02 UTC |
| 9825104 | Eddie Belter | 08 July 2013, 19:43:33 UTC | SomVal: use bam_path instead of merged_alignment_bam_path in align reads | 09 July 2013, 17:26:01 UTC |
| 85eb36c | Eddie Belter | 08 July 2013, 19:42:54 UTC | InstData Aligned Bam Result: rename bam_file to bam_path | 09 July 2013, 17:26:01 UTC |
| f6fdf93 | Eddie Belter | 08 July 2013, 19:09:34 UTC | InstData Merge: create refiner command then call shortcut/execute | 09 July 2013, 17:26:00 UTC |
| 3affef7 | Eddie Belter | 08 July 2013, 19:08:58 UTC | Refine Read GATK: base recalibrator is now base recalibrator bam result | 09 July 2013, 17:26:00 UTC |
