| bc348d1 | APipe Tester | 12 November 2013, 13:16:38 UTC | Updated `genome` tab completion. | 12 November 2013, 13:16:38 UTC |
| 5999ade | APipe Tester | 12 November 2013, 13:15:13 UTC | Updated class browser cache. | 12 November 2013, 13:15:13 UTC |
| 9fd27c4 | Chris Miller | 12 November 2013, 05:28:38 UTC | missing slash in dir path | 12 November 2013, 05:28:38 UTC |
| 4c6bfc8 | Chris Miller | 12 November 2013, 05:10:30 UTC | adding annotation build/directory listings to the help to make life easier | 12 November 2013, 05:10:30 UTC |
| 9c56b54 | Adam Coffman | 11 November 2013, 23:45:41 UTC | allow skipped status for bridge table | 11 November 2013, 23:45:41 UTC |
| 3d0adb3 | Adam Coffman | 11 November 2013, 23:40:46 UTC | sync works for property names other than id | 11 November 2013, 23:40:46 UTC |
| ee4d8ca | Adam Coffman | 11 November 2013, 23:19:59 UTC | only confess if we failed | 11 November 2013, 23:19:59 UTC |
| 689f79e | Adam Coffman | 11 November 2013, 22:59:12 UTC | compiling software is good | 11 November 2013, 22:59:12 UTC |
| 0a42ce2 | Adam Coffman | 11 November 2013, 22:52:59 UTC | start synching analysis project ids via the new bridge entity | 11 November 2013, 22:52:59 UTC |
| e3e32ca | Adam Coffman | 11 November 2013, 22:52:29 UTC | stop syncing analysis project ids over with instrument data | 11 November 2013, 22:52:29 UTC |
| a597e01 | Adam Coffman | 11 November 2013, 22:52:06 UTC | remove references to tgi_lims_status | 11 November 2013, 22:52:06 UTC |
| 10f199a | Adam Coffman | 11 November 2013, 22:50:06 UTC | have CQID use new bridge entity | 11 November 2013, 22:50:06 UTC |
| a80aaf5 | Adam Coffman | 11 November 2013, 22:44:54 UTC | remove AQID | 11 November 2013, 22:44:54 UTC |
| 307e4de | Jason Walker | 11 November 2013, 19:43:01 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 11 November 2013, 19:43:01 UTC |
| 23f197a | Jason Walker | 11 November 2013, 19:42:54 UTC | Add version 2.07.11 of novoalign. | 11 November 2013, 19:42:54 UTC |
| d5a0ba3 | Adam Coffman | 11 November 2013, 19:00:08 UTC | Add instrument data - analysis project bridge table entity. This will faciliate a one instrument data to many analysis projects relationship more easily than using inst data attributes. | 11 November 2013, 19:00:08 UTC |
| 90b7da0 | Thomas Mooney | 11 November 2013, 16:17:16 UTC | Make allow-models-with-builds option not available from command line. | 11 November 2013, 16:17:16 UTC |
| dcf5702 | APipe Tester | 11 November 2013, 13:17:46 UTC | Updated `gmt` tab completion. | 11 November 2013, 13:17:46 UTC |
| 2ca21b4 | APipe Tester | 11 November 2013, 13:17:01 UTC | Updated `genome` tab completion. | 11 November 2013, 13:17:01 UTC |
| 87ebed3 | Chris Miller | 10 November 2013, 23:04:23 UTC | removing genome build option - dangerous since it may not match annotation | 10 November 2013, 23:06:38 UTC |
| c3333f3 | APipe Tester | 09 November 2013, 13:17:42 UTC | Updated `gmt` tab completion. | 09 November 2013, 13:17:42 UTC |
| 5a8ad4c | APipe Tester | 09 November 2013, 13:17:00 UTC | Updated `genome` tab completion. | 09 November 2013, 13:17:00 UTC |
| b27e2d7 | APipe Tester | 09 November 2013, 13:15:21 UTC | Updated class browser cache. | 09 November 2013, 13:15:21 UTC |
| 39d555b | Gabriel Sanderson | 08 November 2013, 23:38:26 UTC | Merge branch 'rnaseq' into gb_master | 08 November 2013, 23:38:26 UTC |
| d4c8d64 | Gabriel Sanderson | 08 November 2013, 23:36:43 UTC | Expand the RNASeq.t test to diff workflow xml vs expected | 08 November 2013, 23:36:43 UTC |
| 972f75c | Gabriel Sanderson | 08 November 2013, 21:39:58 UTC | Merge branch 'normalize' into gb_master | 08 November 2013, 21:39:58 UTC |
| dbc96b0 | Gabriel Sanderson | 08 November 2013, 21:38:59 UTC | Added BackfillIndelVcfHelper which is necessary for my last commit. | 08 November 2013, 21:38:59 UTC |
| 507c8ae | Gabriel Sanderson | 08 November 2013, 21:37:41 UTC | Merge branch 'normalize' into gb_master | 08 November 2013, 21:37:41 UTC |
| 26bed45 | Gabriel Sanderson | 08 November 2013, 21:36:52 UTC | Normalize indels during indel backfill operations for AP-151. | 08 November 2013, 21:36:52 UTC |
| c00a168 | Eddie Belter | 08 November 2013, 19:05:11 UTC | SomVal: add known sites input to allow model copy and updte to capture this input. | 08 November 2013, 19:05:18 UTC |
| 58b630c | Gabriel Sanderson | 08 November 2013, 18:05:29 UTC | Merge branch 'crosssampleindel' into gb_master | 08 November 2013, 18:05:29 UTC |
| f1918b6 | Gabriel Sanderson | 08 November 2013, 17:58:17 UTC | Add varscan_version as a param to CreateCrossSampleIndels | 08 November 2013, 18:04:39 UTC |
| d0294a5 | Gabriel Sanderson | 08 November 2013, 17:58:00 UTC | Remove unused BackfillIndelVcf xml | 08 November 2013, 18:04:39 UTC |
| 5caf816 | dmorton | 08 November 2013, 17:55:35 UTC | Rnaseq test model should diff clean now | 08 November 2013, 17:55:35 UTC |
| 939e137 | dmorton | 08 November 2013, 16:49:20 UTC | Fix silly mistake | 08 November 2013, 17:01:38 UTC |
| affc0dc | dmorton | 08 November 2013, 15:27:51 UTC | DetectFusions command correctly handels linking software-results | 08 November 2013, 15:30:01 UTC |
| 400ee8e | Travis Abbott | 08 November 2013, 14:43:36 UTC | improve filter-structures test: look at actual rows of counts that survive the filter, not just the gene names. | 08 November 2013, 14:43:36 UTC |
| 707a2ae | Travis Abbott | 08 November 2013, 14:43:19 UTC | 1 at end of module | 08 November 2013, 14:43:19 UTC |
| be869aa | Travis Abbott | 08 November 2013, 14:32:13 UTC | change edge-r filter-structures params: specify percentile/min_count in terms of what it takes to fail the filter (as opposed to survive) & update docs accordingly. | 08 November 2013, 14:32:13 UTC |
| ae1b873 | Travis Abbott | 08 November 2013, 14:22:58 UTC | add help messages to edge-r filter-structures | 08 November 2013, 14:22:58 UTC |
| fb5cd9e | Travis Abbott | 08 November 2013, 14:18:37 UTC | add FilterStructures command for edgeR | 08 November 2013, 14:18:37 UTC |
| c41a804 | APipe Tester | 08 November 2013, 13:15:35 UTC | Updated `genome` tab completion. | 08 November 2013, 13:16:21 UTC |
| 9af5eb7 | APipe Tester | 08 November 2013, 13:14:11 UTC | Updated class browser cache. | 08 November 2013, 13:16:20 UTC |
| 82d7414 | dmorton | 08 November 2013, 13:15:08 UTC | Fix lookup for picard_version While it is a model parameter, and hence a build parameter, it is only on the model so it can be specified in the processing-profile. This is misleading imo. | 08 November 2013, 13:15:08 UTC |
| 680bd32 | dmorton | 08 November 2013, 07:17:26 UTC | Complete transition of chimerascan to a workflow | 08 November 2013, 07:17:26 UTC |
| ce4358d | dmorton | 08 November 2013, 04:43:02 UTC | Fix package name and class name mistakes | 08 November 2013, 04:43:02 UTC |
| c6fd82a | Eddie Belter | 07 November 2013, 18:22:40 UTC | RNA Seq: need to pass build into map_workflow_inputs | 07 November 2013, 18:22:40 UTC |
| 825727f | Gabriel Sanderson | 07 November 2013, 17:02:41 UTC | Merge branch 'master' into gb_master | 07 November 2013, 17:02:41 UTC |
| 668f89d | Gabriel Sanderson | 07 November 2013, 17:01:24 UTC | Ignore tabix files in control_variants_for_loh also. | 07 November 2013, 17:01:24 UTC |
| af7c061 | Thomas Mooney | 07 November 2013, 14:59:04 UTC | Add a default of 0 for kb requested. If a desired value is not passed and `du` returns 0, List::Util::max returns undef instead of 0. | 07 November 2013, 14:59:04 UTC |
| bd40e47 | APipe Tester | 07 November 2013, 13:17:02 UTC | Updated `gmt` tab completion. | 07 November 2013, 13:17:02 UTC |
| a45fb38 | APipe Tester | 07 November 2013, 13:16:21 UTC | Updated `genome` tab completion. | 07 November 2013, 13:16:21 UTC |
| db8996f | APipe Tester | 07 November 2013, 13:14:58 UTC | Updated class browser cache. | 07 November 2013, 13:14:58 UTC |
| b9d2bda | Travis Abbott | 07 November 2013, 01:00:38 UTC | doc/formatting updates for edge-r | 07 November 2013, 01:01:28 UTC |
| a47dc5b | Thomas Mooney | 06 November 2013, 23:35:11 UTC | Remove exit()s from error conditions. | 06 November 2013, 23:35:11 UTC |
| 3976a96 | Thomas Mooney | 06 November 2013, 23:28:07 UTC | Ignore files with BAM paths in them. | 06 November 2013, 23:28:07 UTC |
| 39d55e5 | Travis Abbott | 06 November 2013, 22:49:34 UTC | more doc formatting for edge-r classic | 06 November 2013, 22:49:34 UTC |
| bbd19ce | Travis Abbott | 06 November 2013, 22:45:12 UTC | add example output to edge-r help | 06 November 2013, 22:45:12 UTC |
| 9e932b4 | Travis Abbott | 06 November 2013, 22:41:58 UTC | forgot to add test case for edgeR ... | 06 November 2013, 22:41:58 UTC |
| f733b1d | Travis Abbott | 06 November 2013, 22:40:54 UTC | row names now get a (blank) column header in edgeR output | 06 November 2013, 22:40:54 UTC |
| 760ac8e | Travis Abbott | 06 November 2013, 22:36:18 UTC | add a few comments to edge-r test | 06 November 2013, 22:36:18 UTC |
| 0c30ad6 | Travis Abbott | 06 November 2013, 22:29:20 UTC | don't use is_many for groups property not sure if is_many always guarantees that order is preserved | 06 November 2013, 22:29:20 UTC |
| a2e9587 | Travis Abbott | 06 November 2013, 22:02:33 UTC | update edge-r classic docs include description of output format | 06 November 2013, 22:02:33 UTC |
| fd593a6 | Travis Abbott | 06 November 2013, 21:52:09 UTC | update edge-r classic to include class predictions | 06 November 2013, 21:53:07 UTC |
| adb4f43 | Gabriel Sanderson | 06 November 2013, 21:29:50 UTC | Merge branch 'tbi' into gb_master | 06 November 2013, 21:29:50 UTC |
| 1df4e32 | Gabriel Sanderson | 06 November 2013, 21:29:13 UTC | Ignore tabix files since they diff every time. | 06 November 2013, 21:29:38 UTC |
| 304cb00 | Mark Burnett | 06 November 2013, 21:04:10 UTC | bugfix: move is_x queries to subclasses | 06 November 2013, 21:26:39 UTC |
| 35dcdb1 | Avinash Ramu | 06 November 2013, 21:24:37 UTC | added chimerascan filter-output and intersect-sv to clinseq | 06 November 2013, 21:24:52 UTC |
| e9e2723 | Travis Abbott | 06 November 2013, 21:18:03 UTC | add gmt edge-r classic command for diff. exp. analysis | 06 November 2013, 21:18:03 UTC |
| 732f15f | Eddie Belter | 06 November 2013, 20:01:14 UTC | RNA Seq: correctly get workflow inputs for chimerascan command | 06 November 2013, 20:01:14 UTC |
| 6efcfbe | Jim Weible | 06 November 2013, 19:50:03 UTC | prevent the step from crashing on empty input file | 06 November 2013, 19:50:10 UTC |
| 325119e | Mark Burnett | 06 November 2013, 19:08:03 UTC | WorkflowBuilder::Command verifies specified command class | 06 November 2013, 19:09:58 UTC |
| 93d974a | Thomas Mooney | 06 November 2013, 18:35:20 UTC | Make this a more sensical UR class definition. | 06 November 2013, 18:35:20 UTC |
| 4c785ec | Thomas Mooney | 06 November 2013, 18:21:38 UTC | Match name in link to that of the input property. | 06 November 2013, 18:21:38 UTC |
| 98e5459 | Thomas Mooney | 06 November 2013, 14:45:43 UTC | Update somval blessed build. Includes: indel VCF, tabix, and SV validation files | 06 November 2013, 14:45:43 UTC |
| b6daa70 | Gabriel Sanderson | 06 November 2013, 03:46:18 UTC | Merge branch 'blessed' into gb_master | 06 November 2013, 03:46:18 UTC |
| b01b03a | Gabriel Sanderson | 06 November 2013, 03:45:27 UTC | Updated build diffs for tabix files. | 06 November 2013, 03:45:27 UTC |
| 8bb943b | Thomas Mooney | 05 November 2013, 23:05:04 UTC | whitespace only | 05 November 2013, 23:05:04 UTC |
| ccc4e35 | Thomas Mooney | 05 November 2013, 22:18:02 UTC | Someone changed this in the database. | 05 November 2013, 22:18:02 UTC |
| cf0e4e3 | Gabriel Sanderson | 05 November 2013, 21:23:39 UTC | Merge branch 'blessed' into gb_master | 05 November 2013, 21:23:39 UTC |
| 5c107a9 | Gabriel Sanderson | 05 November 2013, 21:23:15 UTC | updated expected somatic-validation-sv output for varscan-somatic-validation now providing indel vcfs | 05 November 2013, 21:23:15 UTC |
| 1b290c7 | Eddie Belter | 05 November 2013, 21:04:40 UTC | Varscan Somatic: add reference and indel filter somatic statuses to indel to match snv | 05 November 2013, 21:04:40 UTC |
| e8948d8 | Travis Abbott | 05 November 2013, 18:45:54 UTC | add format_transcripts method to VepConsequenceParser this re-formats a parsed transcript hash as a CSQ info string. | 05 November 2013, 18:45:54 UTC |
| 9f25dfe | Travis Abbott | 05 November 2013, 17:44:37 UTC | Update docs for GF::Vcf::Entry | 05 November 2013, 17:52:02 UTC |
| 919e1ab | APipe Tester | 05 November 2013, 13:17:40 UTC | Updated `gmt` tab completion. | 05 November 2013, 13:17:40 UTC |
| 1026e2d | APipe Tester | 05 November 2013, 13:16:50 UTC | Updated `genome` tab completion. | 05 November 2013, 13:16:50 UTC |
| d4c433c | APipe Tester | 05 November 2013, 13:14:55 UTC | Updated class browser cache. | 05 November 2013, 13:14:55 UTC |
| 7b6680c | Travis Abbott | 04 November 2013, 22:58:11 UTC | add filtering to Vep Consequence Parser. | 04 November 2013, 22:58:31 UTC |
| 620e672 | Jason Walker | 04 November 2013, 22:19:54 UTC | A warning message if the junctions output is not found in a build for a model. | 04 November 2013, 22:19:54 UTC |
| e00ec25 | Adam Coffman | 04 November 2013, 21:57:52 UTC | small changes related to purging | 04 November 2013, 21:57:52 UTC |
| 8d3e751 | Chris Miller | 04 November 2013, 21:38:29 UTC | adding VCF convertors for varscan-somatic-validation | 04 November 2013, 21:51:06 UTC |
| 6662cad | dmorton | 04 November 2013, 21:39:30 UTC | DetectFusions command has input of build_id instead of build | 04 November 2013, 21:41:58 UTC |
| 55b2955 | Chris Miller | 04 November 2013, 21:35:47 UTC | doc updates | 04 November 2013, 21:36:00 UTC |
| 96e733b | dmorton | 04 November 2013, 21:23:20 UTC | Fix silly mistakes | 04 November 2013, 21:23:50 UTC |
| 0ac5f2b | Mark Burnett | 04 November 2013, 20:49:59 UTC | rename id to allocation_id | 04 November 2013, 21:17:54 UTC |
| d12c8c4 | dmorton | 04 November 2013, 21:13:36 UTC | Chimerascan builds and executes workflow | 04 November 2013, 21:14:46 UTC |
| 50031f1 | dmorton | 04 November 2013, 18:21:56 UTC | Make Result directory structure echo Command structure | 04 November 2013, 21:14:46 UTC |
| e314172 | dmorton | 04 November 2013, 18:12:24 UTC | Pull decision logic out of RnaSeq Model DetectFusions command now determines what commands to fire off to do fusion detection based on the parameters it is passed. | 04 November 2013, 21:14:45 UTC |
| 25ac471 | dmorton | 04 November 2013, 17:22:48 UTC | Reimagined directory structure yet again | 04 November 2013, 21:14:45 UTC |
| db86a76 | dmorton | 04 November 2013, 16:45:12 UTC | Rearrange directory structure for Chimerascan Commands | 04 November 2013, 21:14:44 UTC |
