| 2510af8 | Chris Miller | 02 January 2013, 15:50:03 UTC | updating bam-window path | 02 January 2013, 15:50:03 UTC |
| 73248cf | Thomas Mooney | 31 December 2012, 22:27:25 UTC | Match large indel BAM diffs by regex. | 31 December 2012, 22:27:25 UTC |
| 723d858 | Chris Miller | 31 December 2012, 20:57:17 UTC | adding a DV2 module for bam-window - windowed readcounts | 31 December 2012, 20:57:34 UTC |
| c60dd04 | Thomas Mooney | 31 December 2012, 20:23:00 UTC | Reduce CPU request since can only use 2 CPUs at present. | 31 December 2012, 20:23:00 UTC |
| dcdbc61 | Thomas Mooney | 31 December 2012, 18:51:11 UTC | Cleanup error handling: $self not self, die not exit. | 31 December 2012, 18:51:11 UTC |
| 7a89af9 | APipe Tester | 31 December 2012, 18:09:11 UTC | updated ur submodule to 1a27ed4 | 31 December 2012, 18:09:11 UTC |
| f29bdeb | Thomas Mooney | 31 December 2012, 16:59:19 UTC | Skip tests if license has expired. | 31 December 2012, 16:59:19 UTC |
| a19e439 | Thomas Mooney | 31 December 2012, 15:07:15 UTC | More hard-coded paths... add the PATH to the executables this pipeline uses. | 31 December 2012, 15:07:15 UTC |
| 6d5f2ef | Jim Weible | 31 December 2012, 14:16:12 UTC | allow somatic validation commands to pass and do nothing if tier variants has no tiering version | 31 December 2012, 14:16:19 UTC |
| 6bb8a91 | Gabriel Sanderson | 29 December 2012, 05:45:55 UTC | Merge branch 'validation' into gb_master | 29 December 2012, 05:45:55 UTC |
| 9750742 | Gabriel Sanderson | 29 December 2012, 02:13:46 UTC | Refactor ValidateSmallIndels to implement a workflow to parallelize things. | 29 December 2012, 05:44:18 UTC |
| 1415144 | Chris Miller | 28 December 2012, 17:24:29 UTC | fixing broken test | 28 December 2012, 17:24:36 UTC |
| d3308cb | Beifang Niu | 28 December 2012, 16:44:04 UTC | add mutation spectrum tool | 28 December 2012, 16:44:04 UTC |
| 05c0cf1 | Chris Miller | 27 December 2012, 22:14:50 UTC | adding test for BamWindow | 27 December 2012, 22:14:50 UTC |
| 5b8890c | apregier | 27 December 2012, 21:53:30 UTC | Merge branch 'fix' into gb_master | 27 December 2012, 21:53:30 UTC |
| 0606ef1 | apregier | 27 December 2012, 21:53:16 UTC | Ignore files with bam paths for large indel validation | 27 December 2012, 21:53:16 UTC |
| 3fea7ec | apregier | 27 December 2012, 21:49:25 UTC | Merge branch 'fix' into gb_master | 27 December 2012, 21:49:25 UTC |
| f76770a | apregier | 27 December 2012, 21:49:09 UTC | Fix build diffs for somatic validation lage indels | 27 December 2012, 21:49:09 UTC |
| 4addc89 | apregier | 27 December 2012, 20:39:14 UTC | Merge branch 'fix' into gb_master | 27 December 2012, 20:39:14 UTC |
| 2d40da8 | apregier | 27 December 2012, 20:30:03 UTC | Make inputs optional so that skip option is functional | 27 December 2012, 20:38:54 UTC |
| bb57624 | Chris Miller | 27 December 2012, 20:21:02 UTC | namefix | 27 December 2012, 20:21:02 UTC |
| 384945e | Chris Miller | 27 December 2012, 19:56:44 UTC | blew away a bunch of legacy code and modified this to be a simple wrapper around the new bam-window c program. Will update the absolute path to the executable after it is installed system-wide | 27 December 2012, 19:56:44 UTC |
| 181d90e | Chris Miller | 27 December 2012, 18:36:59 UTC | initial commit of CopyCat for paired tumor/normal samples | 27 December 2012, 18:37:07 UTC |
| 97941a8 | apregier | 27 December 2012, 17:15:43 UTC | Merge branch 'fix' into gb_master | 27 December 2012, 17:15:43 UTC |
| 2d432a4 | apregier | 27 December 2012, 17:13:42 UTC | Set reference_build_id even if we are skipping | 27 December 2012, 17:15:25 UTC |
| f7ac339 | apregier | 27 December 2012, 17:09:54 UTC | Merge branch 'fix' into gb_master | 27 December 2012, 17:09:54 UTC |
| 3099bb1 | apregier | 27 December 2012, 17:09:22 UTC | Set output_dir even if we skip large indel validation | 27 December 2012, 17:09:32 UTC |
| fd1d78f | Adam Coffman | 27 December 2012, 16:49:22 UTC | Remove role check for archiving and unarchiving | 27 December 2012, 16:49:22 UTC |
| 6f968b5 | Thomas Mooney | 27 December 2012, 15:08:33 UTC | Require a reason for queueing, just like with the plain "queue" command. | 27 December 2012, 15:08:33 UTC |
| 597fae9 | Thomas Mooney | 27 December 2012, 14:32:58 UTC | These properties were long added to the class--remove the backfill | 27 December 2012, 14:32:58 UTC |
| 247e666 | apregier | 26 December 2012, 22:18:35 UTC | Merge branch 'fix' into gb_master | 26 December 2012, 22:18:35 UTC |
| c201d86 | apregier | 26 December 2012, 18:51:42 UTC | Refactor to avoid creating refalign builds for large indel validation | 26 December 2012, 22:17:48 UTC |
| e7c8f4e | Thomas Mooney | 26 December 2012, 21:21:28 UTC | Skip in SomaticValidation in single-sample case. | 26 December 2012, 21:21:28 UTC |
| 22c75cc | apregier | 26 December 2012, 16:40:50 UTC | Merge branch 'fix' into gb_master | 26 December 2012, 16:40:50 UTC |
| 2aa19fd | apregier | 24 December 2012, 20:01:27 UTC | Factor out generation of assembly fastas for long indel validation | 26 December 2012, 16:40:36 UTC |
| 4028082 | Thomas Mooney | 26 December 2012, 16:38:33 UTC | Since build is (strangely) optional, only skip if we have one. | 26 December 2012, 16:38:33 UTC |
| 0c8dc56 | Thomas Mooney | 26 December 2012, 16:07:13 UTC | Pass the SomVal build directly--otherwise we'd grab the wrong one (or none) | 26 December 2012, 16:07:13 UTC |
| 9e9e564 | Thomas Mooney | 26 December 2012, 15:55:33 UTC | Just skip if in single-sample mode. | 26 December 2012, 15:55:33 UTC |
| 9111b86 | APipe Tester | 24 December 2012, 20:06:20 UTC | updated ur submodule to 9104537 | 24 December 2012, 20:06:20 UTC |
| 6ef1194 | apregier | 24 December 2012, 19:54:14 UTC | Merge branch 'fix' into gb_master | 24 December 2012, 19:54:14 UTC |
| 5d4a9d2 | apregier | 24 December 2012, 19:53:38 UTC | Update test to compare files | 24 December 2012, 19:54:01 UTC |
| 381d568 | Eddie Belter | 24 December 2012, 19:01:51 UTC | MC16s: run status outputs a line for ignored/skipped inst data | 24 December 2012, 19:01:51 UTC |
| 5167272 | apregier | 24 December 2012, 18:50:01 UTC | Merge branch 'fix' into gb_master | 24 December 2012, 18:50:01 UTC |
| 4109d9a | apregier | 24 December 2012, 18:49:41 UTC | Don't write test files to home directory | 24 December 2012, 18:49:41 UTC |
| c116d90 | apregier | 24 December 2012, 15:54:10 UTC | Merge branch 'fix' into gb_master | 24 December 2012, 15:54:10 UTC |
| c4e4c55 | apregier | 21 December 2012, 17:01:52 UTC | Factor out processing of realigned reads in long indel validation | 24 December 2012, 15:51:31 UTC |
| 8e98317 | Nathan Nutter | 22 December 2012, 17:14:46 UTC | add TestTracker config | 22 December 2012, 17:14:46 UTC |
| 921e141 | Nathan Nutter | 22 December 2012, 02:58:22 UTC | whitespace | 22 December 2012, 02:58:44 UTC |
| f808fa4 | Nathan Nutter | 22 December 2012, 02:58:03 UTC | fix void context warning | 22 December 2012, 02:58:43 UTC |
| 411f82b | dmorton | 21 December 2012, 17:39:56 UTC | Add option to Gatk/RealignIndels.pm to make bam index Remove step in ValidateSmallIndels that was doing the same. | 21 December 2012, 17:39:56 UTC |
| 96b9830 | dmorton | 21 December 2012, 17:12:40 UTC | Remove Utility::Text from Sys.pm It wasn't being used. | 21 December 2012, 17:14:10 UTC |
| 60e461e | Jason Walker | 21 December 2012, 17:12:53 UTC | Add the deduplication_handler param for RnaSeq models. | 21 December 2012, 17:12:53 UTC |
| cc07cd3 | Gabriel Sanderson | 21 December 2012, 00:32:30 UTC | Merge branch 'polymuttheaderfix' into gb_master | 21 December 2012, 00:32:30 UTC |
| 3d003df | Gabriel Sanderson | 21 December 2012, 00:32:15 UTC | Add a couple more header fixes. We should no longer have duplicate DQ or missing DS headers | 21 December 2012, 00:32:22 UTC |
| 8c1ab9d | Gabriel Sanderson | 21 December 2012, 00:05:03 UTC | Merge branch 'master' into gb_master | 21 December 2012, 00:05:03 UTC |
| 4dfc246 | Gabriel Sanderson | 21 December 2012, 00:04:54 UTC | Fixed a spammy common warning | 21 December 2012, 00:04:59 UTC |
| 8d3fb4d | Gabriel Sanderson | 21 December 2012, 00:01:16 UTC | Merge branch 'validation' into gb_master | 21 December 2012, 00:01:16 UTC |
| 4a1f154 | Gabriel Sanderson | 21 December 2012, 00:01:02 UTC | Added a test case for gmt gatk realign-indels. | 21 December 2012, 00:01:02 UTC |
| f9af56c | Gabriel Sanderson | 20 December 2012, 21:38:07 UTC | Merge branch 'validation' into gb_master | 20 December 2012, 21:38:07 UTC |
| efb19f0 | Gabriel Sanderson | 20 December 2012, 21:19:33 UTC | Added a gmt gatk realign-indels command to run -T IndelRealigner. ValidateSmallIndels is refactored to use this new command. Added some functionality to gmt gatk to be more useful as a base class. | 20 December 2012, 21:38:00 UTC |
| 8c2cc78 | Thomas Mooney | 20 December 2012, 21:06:21 UTC | Tighten the regexes now that there are two alignment directories. | 20 December 2012, 21:06:55 UTC |
| 2cf0e7b | Jim Weible | 20 December 2012, 21:03:14 UTC | Serialize the uniprot mapping | 20 December 2012, 21:03:20 UTC |
| 6f800f3 | Nathan Dees | 20 December 2012, 16:34:35 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 December 2012, 16:34:35 UTC |
| 99c3e87 | Nathan Dees | 20 December 2012, 16:34:30 UTC | new joinx version plus case-independent checking of ref sequence at cpg loci | 20 December 2012, 16:34:30 UTC |
| ba54aac | Feiyu Du | 20 December 2012, 16:07:20 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 December 2012, 16:07:20 UTC |
| 025661f | Feiyu Du | 20 December 2012, 16:06:46 UTC | add FT subfield to FORMAT and populate it in sample columns for strelka detector vcf output | 20 December 2012, 16:06:46 UTC |
| a58e614 | Thomas Mooney | 20 December 2012, 14:18:16 UTC | Only require a reference if we're going to run the step. | 20 December 2012, 14:18:16 UTC |
| 8310a2d | Gabriel Sanderson | 19 December 2012, 23:41:18 UTC | Merge branch 'validation' into gb_master | 19 December 2012, 23:41:18 UTC |
| 0516d90 | Gabriel Sanderson | 19 December 2012, 23:41:04 UTC | Refactored the a section of code in PullOneTwoBpIndels that is relevant for SomaticValidation models into a new module in G:M:SomaticValidation::Command::ValidateSmallIndels. | 19 December 2012, 23:41:14 UTC |
| 9a2a45f | Thomas Mooney | 19 December 2012, 23:16:52 UTC | Fix typo. | 19 December 2012, 23:16:52 UTC |
| 5a7168d | Gabriel Sanderson | 19 December 2012, 22:56:54 UTC | Merge branch 'master' into gb_master | 19 December 2012, 22:56:54 UTC |
| de5a57f | Gabriel Sanderson | 19 December 2012, 22:56:40 UTC | The previous commit did not actually include AD and BQ information in the vcf line. Fixed this and updated the test case | 19 December 2012, 22:56:46 UTC |
| 7755e2a | Malachi Griffith | 19 December 2012, 22:51:32 UTC | clinseq - fixed summarize-builds to get samples associated with a clinseq model more accurately | 19 December 2012, 22:51:32 UTC |
| 60b07ab | Malachi Griffith | 19 December 2012, 22:50:56 UTC | CnView - added plot that is scaled consistently and more suitable for comparison across multiple tumors | 19 December 2012, 22:50:56 UTC |
| 8a896f3 | Thomas Mooney | 19 December 2012, 22:27:55 UTC | Split SV validation into steps to eliminate nested refalign model. The reference-sequence generation still delegates to a new build. It was moved to a separate step in order to have it be committed before the alignments try to use it. | 19 December 2012, 22:27:55 UTC |
| a05338c | Thomas Mooney | 19 December 2012, 22:24:30 UTC | Prevent a few failures in error handling. A nested workflow in a pure-workflow build may match the three-part format without having an event or stage for each step, so just bail if we don't get something that looks like an ID. | 19 December 2012, 22:24:30 UTC |
| 451cf39 | Gabriel Sanderson | 19 December 2012, 21:36:11 UTC | Merge branch 'master' into gb_master | 19 December 2012, 21:36:11 UTC |
| 6acd2e3 | Gabriel Sanderson | 19 December 2012, 21:36:02 UTC | Reversing a hack in order to try something else | 19 December 2012, 21:36:02 UTC |
| d8892dc | APipe Tester | 19 December 2012, 21:20:17 UTC | updated ur submodule to 7dec1ff | 19 December 2012, 21:20:17 UTC |
| a76407b | Gabriel Sanderson | 19 December 2012, 21:17:03 UTC | Merge branch 'master' into gb_master | 19 December 2012, 21:17:03 UTC |
| 851c457 | Gabriel Sanderson | 19 December 2012, 21:16:47 UTC | Updated test data | 19 December 2012, 21:16:47 UTC |
| 478181e | Ben Oberkfell | 19 December 2012, 20:57:31 UTC | dont auto-abort for bad postgres driver if you are running a LIMS command, because you still have to use ancient perl to run it. | 19 December 2012, 20:57:31 UTC |
| 2603e2b | Ben Oberkfell | 19 December 2012, 20:56:43 UTC | always use genome-perl when shelling out. | 19 December 2012, 20:56:43 UTC |
| 35594cc | Ben Oberkfell | 19 December 2012, 20:20:36 UTC | Merge branch 'master' of git:/srv/git/genome | 19 December 2012, 20:20:36 UTC |
| 6ec0fc4 | Ben Oberkfell | 19 December 2012, 20:20:30 UTC | make new picard module available | 19 December 2012, 20:20:30 UTC |
| c19ebb8 | Gabriel Sanderson | 19 December 2012, 19:41:07 UTC | Merge branch 'master' into gb_master | 19 December 2012, 19:41:07 UTC |
| 52a586d | Gabriel Sanderson | 19 December 2012, 19:40:47 UTC | Increment vcf version. | 19 December 2012, 19:40:47 UTC |
| 2c5284d | Ben Oberkfell | 19 December 2012, 17:38:36 UTC | fix postgres syncing on sample attribute stomper for real | 19 December 2012, 17:38:50 UTC |
| 4bb4333 | Dan Koboldt | 19 December 2012, 17:33:13 UTC | Changes to improve the way VarScan output is converted to VCF fields | 19 December 2012, 17:33:13 UTC |
| a52c018 | Dan Koboldt | 19 December 2012, 17:01:16 UTC | Updated line 34 to force PhenotypeCorrelation models to always proceed as if QC-passed | 19 December 2012, 17:01:16 UTC |
| 8203901 | Thomas Mooney | 19 December 2012, 14:12:55 UTC | Add category to the newer somatic-validation pipeline steps. | 19 December 2012, 14:12:55 UTC |
| 5cc9590 | Malachi Griffith | 19 December 2012, 01:21:04 UTC | clinseq: update to converge scripts - added SV fusion converge script | 19 December 2012, 01:21:04 UTC |
| ee0d3d3 | apregier | 18 December 2012, 23:08:11 UTC | Merge branch 'fix' into gb_master | 18 December 2012, 23:08:11 UTC |
| 5deb7f1 | apregier | 18 December 2012, 23:07:51 UTC | Get the tiering directory from the annotation build | 18 December 2012, 23:07:51 UTC |
| dacd33b | apregier | 18 December 2012, 23:03:18 UTC | Merge branch 'fix' into gb_master | 18 December 2012, 23:03:18 UTC |
| 0d12c3d | apregier | 18 December 2012, 23:02:43 UTC | Fix CountContigs command so it handles contig names with parens | 18 December 2012, 23:02:56 UTC |
| c7517c3 | Gabriel Sanderson | 18 December 2012, 21:36:36 UTC | Merge branch 'validation' into gb_master | 18 December 2012, 21:36:36 UTC |
| 87f7d0c | Gabriel Sanderson | 17 December 2012, 22:53:49 UTC | Add run-inline option to PullOneTwoBpIndels so that one part may be run inline for testing purposes. Added a test case | 18 December 2012, 21:35:21 UTC |
| 0afbb87 | Eddie Belter | 18 December 2012, 21:00:51 UTC | MC16s: process inst data event calls seq platform on model | 18 December 2012, 21:04:15 UTC |
| ba7ac37 | Malachi Griffith | 18 December 2012, 20:23:43 UTC | ClinSeq: various patches to fix converge steps broken by recent updates to the pipeline | 18 December 2012, 20:23:43 UTC |
