e86acd0 | Thomas Mooney | 03 January 2013, 19:26:11 UTC | Use Picard to convert the merged BAM into two FASTQs directly. Additionally, this re-reverses negative-strand reads back to their original version and doesn't print duplicate reads for multiple alignments. | 03 January 2013, 19:26:11 UTC |
26d36db | Thomas Mooney | 03 January 2013, 19:02:04 UTC | Add a command wrapper for the unmodified picard "SamToFastq" command. | 03 January 2013, 19:02:04 UTC |
3008364 | Thomas Mooney | 03 January 2013, 19:01:28 UTC | Edit the help to reflect that this isn't the real Picard SamToFastq command. | 03 January 2013, 19:01:28 UTC |
77cfa9c | Thomas Mooney | 03 January 2013, 16:12:55 UTC | fix typo same => sam | 03 January 2013, 16:12:55 UTC |
7ae48a3 | Thomas Mooney | 03 January 2013, 16:12:34 UTC | Remove some redundant information from docs. | 03 January 2013, 16:12:34 UTC |
3e4a358 | Scott Smith | 03 January 2013, 16:03:30 UTC | moved druggable gene logic from the module body into the execute() method | 03 January 2013, 16:03:30 UTC |
42d24f9 | Nathan Nutter | 03 January 2013, 00:59:19 UTC | add test_regex to .test-tracker.conf | 03 January 2013, 01:00:34 UTC |
bb84433 | Eddie Belter | 03 January 2013, 00:50:47 UTC | Stie TGI Org Sample: typo in props to copy | 03 January 2013, 00:51:00 UTC |
47e32bf | Obi Griffith | 03 January 2013, 00:49:57 UTC | added option to upper case or not for alternate gene names to all importers | 03 January 2013, 00:49:57 UTC |
4225996 | Eddie Belter | 02 January 2013, 20:55:19 UTC | Build: uniq allocations from all_allocations | 02 January 2013, 20:55:19 UTC |
4ef1d0a | Eddie Belter | 02 January 2013, 20:41:30 UTC | Build Unarchive: unarchives and relinks symlinked alloations | 02 January 2013, 20:41:45 UTC |
e444ff0 | Eddie Belter | 02 January 2013, 20:40:45 UTC | Build: add getting symlinked allocations in all_allocations and add method to attempt to relink broken ones | 02 January 2013, 20:41:44 UTC |
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 |