| 200b089 | Thomas Mooney | 29 June 2013, 23:34:13 UTC | Make sure we operate on the class name and not an object. | 29 June 2013, 23:34:13 UTC |
| f25da58 | apregier | 28 June 2013, 22:23:58 UTC | Update blessed build for gene prediction | 28 June 2013, 22:23:58 UTC |
| 744a4c3 | APipe Tester | 28 June 2013, 22:09:47 UTC | Updated `gmt` tab completion. | 28 June 2013, 22:09:59 UTC |
| e876b81 | APipe Tester | 28 June 2013, 22:08:55 UTC | Updated `genome` tab completion. | 28 June 2013, 22:09:59 UTC |
| 9084033 | APipe Tester | 28 June 2013, 22:07:17 UTC | Updated class browser cache. | 28 June 2013, 22:09:59 UTC |
| 3842b55 | Scott Smith | 28 June 2013, 22:03:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 22:03:30 UTC |
| 8bc25e6 | Scott Smith | 28 June 2013, 22:03:15 UTC | made the CosmicOmim.pm tool compatible with new genome-db-cosmic structure, containing multiple data sets besides the original gene CSV files. | 28 June 2013, 22:03:15 UTC |
| 833b408 | Adam Coffman | 28 June 2013, 21:59:59 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:59:59 UTC |
| b445043 | Adam Coffman | 28 June 2013, 21:59:40 UTC | whitespace | 28 June 2013, 21:59:40 UTC |
| d34b8d8 | Scott Smith | 28 June 2013, 21:53:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:53:10 UTC |
| cd5a629 | Scott Smith | 28 June 2013, 21:52:58 UTC | gmt phred-phrap has a base class, and that module also has a base class. The later was used as the tree delegator, but is being renamed in this commit, with a title befitting its absurdities. | 28 June 2013, 21:52:58 UTC |
| f4cc365 | Scott Smith | 28 June 2013, 21:45:46 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:45:46 UTC |
| 2a2c0c0 | Scott Smith | 28 June 2013, 21:44:33 UTC | bleassed new clinseq build | 28 June 2013, 21:44:33 UTC |
| 212a0d5 | Malachi Griffith | 28 June 2013, 21:35:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:35:10 UTC |
| e1c8fdd | Malachi Griffith | 28 June 2013, 21:34:51 UTC | Fix option to specify no file extension in abi-to-scf | 28 June 2013, 21:34:51 UTC |
| 8df557f | Adam Coffman | 28 June 2013, 21:15:31 UTC | switch explicit lister to genome command crud | 28 June 2013, 21:15:31 UTC |
| d3b9ea9 | Adam Coffman | 28 June 2013, 21:06:05 UTC | add explicit create command | 28 June 2013, 21:06:05 UTC |
| 7345416 | Adam Coffman | 28 June 2013, 20:58:49 UTC | improve cascading delete | 28 June 2013, 20:58:49 UTC |
| cfaf76f | Adam Coffman | 28 June 2013, 20:58:20 UTC | use genome command crud instead of explicit lister | 28 June 2013, 20:58:20 UTC |
| d15e641 | APipe Tester | 28 June 2013, 20:55:34 UTC | updated ur submodule to cd3861c | 28 June 2013, 20:55:34 UTC |
| 2ad85c1 | APipe Tester | 28 June 2013, 19:30:38 UTC | Updated `genome` tab completion. | 28 June 2013, 19:30:38 UTC |
| 986ccdc | APipe Tester | 28 June 2013, 19:28:26 UTC | Updated class browser cache. | 28 June 2013, 19:28:26 UTC |
| ded9691 | Mark Burnett | 28 June 2013, 19:05:27 UTC | use a less fragile test for the GSCApp-RefSeq compatibility test | 28 June 2013, 19:05:27 UTC |
| cda7b97 | Mark Burnett | 28 June 2013, 18:58:22 UTC | fix Define-docs.t expected output for amplicon assembly | 28 June 2013, 18:58:22 UTC |
| 022fde5 | Mark Burnett | 28 June 2013, 17:53:09 UTC | Merge branch 'lims-RefSeq-bug' | 28 June 2013, 17:53:09 UTC |
| 28869f5 | Mark Burnett | 28 June 2013, 17:31:52 UTC | update define docs expected output | 28 June 2013, 17:31:52 UTC |
| b553397 | Eddie Belter | 28 June 2013, 16:29:30 UTC | InstData Import: updates to import SRAs | 28 June 2013, 16:30:05 UTC |
| cd7e2a5 | Eddie Belter | 27 June 2013, 21:45:38 UTC | Sample Manager: do not test sample hash data structure | 28 June 2013, 16:30:04 UTC |
| 4ccaa9f | Eddie Belter | 27 June 2013, 21:44:34 UTC | Sample Manager: store source files as comma delimited string | 28 June 2013, 16:30:04 UTC |
| 94e0e1b | Eddie Belter | 21 June 2013, 19:50:07 UTC | Sample Import Manager: do not display status for build | 28 June 2013, 16:30:04 UTC |
| 8c4deb1 | Eddie Belter | 21 June 2013, 19:31:43 UTC | Sample Import Manager: update status output; fix adding inst data bug | 28 June 2013, 16:30:03 UTC |
| b33f2ed | Eddie Belter | 21 June 2013, 15:29:22 UTC | Sample Import Manager: set job status on sample before make progress and then again when displaying status | 28 June 2013, 16:30:03 UTC |
| 0c64dfd | Eddie Belter | 21 June 2013, 15:24:39 UTC | Sample Import Manager: request build and delete inst data uncommented | 28 June 2013, 16:30:02 UTC |
| b0558f1 | Adam Coffman | 28 June 2013, 16:00:35 UTC | Make AnalysisProject deletions cascade Deleting an analysis project will no longer leave an orphaned configuration set and corresponding allocation. | 28 June 2013, 16:00:35 UTC |
| d1682ad | Adam Coffman | 28 June 2013, 15:59:50 UTC | auto set created_by in the constructor | 28 June 2013, 15:59:50 UTC |
| e37c5cf | Scott Smith | 27 June 2013, 22:22:34 UTC | initial comparison tool examines variant calling results | 27 June 2013, 22:22:34 UTC |
| 3614e51 | Jim Weible | 27 June 2013, 17:52:15 UTC | cleanup | 27 June 2013, 17:52:26 UTC |
| 17668be | Feiyu Du | 27 June 2013, 17:04:41 UTC | approve build diff for som-val, som-var-short and ref-align | 27 June 2013, 17:04:41 UTC |
| 68d3e1f | Mark Burnett | 27 June 2013, 15:27:28 UTC | bugfix: loading RefSeq with GSCApp now works | 27 June 2013, 15:28:35 UTC |
| 3f1cbb8 | Mark Burnett | 27 June 2013, 14:25:55 UTC | refactor: move properties from M:B:ImportedRefSeq to M:B:RefSeq | 27 June 2013, 15:28:35 UTC |
| 85b32b8 | Mark Burnett | 25 June 2013, 18:59:33 UTC | refactor: move M:B:RefSeq to its own file | 27 June 2013, 15:28:34 UTC |
| 22d03e1 | Mark Burnett | 25 June 2013, 18:36:27 UTC | refactor: move G:M:B:ImportedRefSeq to its own file | 27 June 2013, 15:28:33 UTC |
| 133dd2d | Mark Burnett | 25 June 2013, 17:51:20 UTC | refactor: move M:ImportedReferenceSequence to its own file | 27 June 2013, 15:28:33 UTC |
| c48ec48 | Mark Burnett | 25 June 2013, 17:34:40 UTC | update tests to expose broken behavior the broken behavior was introduced by commit: 87727c838b45b1412613a9a5f43086c216f06e09 | 27 June 2013, 15:28:31 UTC |
| af47c0f | APipe Tester | 27 June 2013, 15:24:51 UTC | Updated `gmt` tab completion. | 27 June 2013, 15:24:51 UTC |
| 18297ce | APipe Tester | 27 June 2013, 15:22:54 UTC | Updated `genome` tab completion. | 27 June 2013, 15:22:54 UTC |
| 027f610 | APipe Tester | 27 June 2013, 15:20:30 UTC | Updated class browser cache. | 27 June 2013, 15:20:30 UTC |
| 893a78d | Jim Weible | 26 June 2013, 18:48:25 UTC | cleanup whitespace | 27 June 2013, 13:06:44 UTC |
| bc819d3 | Jim Weible | 26 June 2013, 15:23:27 UTC | cleanup | 27 June 2013, 13:06:43 UTC |
| 7f93350 | Jim Weible | 25 June 2013, 20:00:46 UTC | basic tool to match varscan consensus calls to original vcf indels and build a new vcf file for cross sample indel calling | 27 June 2013, 13:06:42 UTC |
| ce348b9 | Scott Smith | 27 June 2013, 03:32:32 UTC | updated to dv2 BreakdancerMax | 27 June 2013, 03:32:32 UTC |
| 329c095 | Scott Smith | 27 June 2013, 03:27:12 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 June 2013, 03:27:12 UTC |
| a1876a1 | Scott Smith | 27 June 2013, 03:27:04 UTC | clinseq now passes the cosmic database version to the step that creates mutation diagrams | 27 June 2013, 03:27:04 UTC |
| b7dfdcb | Ben Oberkfell | 27 June 2013, 03:20:22 UTC | Put test case data where it belongs. | 27 June 2013, 03:20:22 UTC |
| cb544e9 | APipe Tester | 26 June 2013, 21:35:42 UTC | Updated `genome` tab completion. | 26 June 2013, 21:37:22 UTC |
| 830d908 | APipe Tester | 26 June 2013, 21:32:57 UTC | Updated class browser cache. | 26 June 2013, 21:37:22 UTC |
| a25ec91 | Scott Smith | 26 June 2013, 21:31:08 UTC | updated Genome/Model/ClinSeq/Command/TestGenomeCommands.t to use a new test input data set | 26 June 2013, 21:31:08 UTC |
| fbcf1da | Scott Smith | 26 June 2013, 21:24:45 UTC | update the clinseq model define docs to include new inputs | 26 June 2013, 21:24:45 UTC |
| 1e03c7d | Scott Smith | 26 June 2013, 20:49:06 UTC | Add cancer_annotation_db misc_annotation_db and cosmic_annotation_db to ClinSeq input lists, with current hard-coded values as defaults. No code actually uses these inputs yet. | 26 June 2013, 20:49:06 UTC |
| 4a3eaf0 | Scott Smith | 26 June 2013, 20:03:15 UTC | updated to handle import_iteration "0" | 26 June 2013, 20:03:15 UTC |
| 4781469 | Scott Smith | 26 June 2013, 18:54:05 UTC | fixed typos in new DV2 BreakdancerMax module | 26 June 2013, 18:54:05 UTC |
| a2c6885 | Mark Burnett | 26 June 2013, 16:21:34 UTC | M:T:Anno:TranscriptVar:V3 make temporary parameter variable optional | 26 June 2013, 17:57:47 UTC |
| 9316486 | Travis Abbott | 26 June 2013, 17:43:54 UTC | bless build diffs for indels the previously blessed results were very wrong. | 26 June 2013, 17:43:54 UTC |
| 52326b1 | Eddie Belter | 26 June 2013, 17:22:41 UTC | InstData GATK: add status msgs to show inputs | 26 June 2013, 17:25:45 UTC |
| 5fd36a1 | Eddie Belter | 26 June 2013, 17:19:25 UTC | InstData GATK: was getting indel result twice in known sites | 26 June 2013, 17:25:45 UTC |
| ec45bc5 | Eddie Belter | 18 June 2013, 17:45:24 UTC | InstData Gatk: add known sites snv vcfs to base with knowns; use only known sites indel vcf in indel realigner | 26 June 2013, 17:25:44 UTC |
| f4232c7 | Eddie Belter | 17 June 2013, 15:21:03 UTC | InstData GATK: realloc allocation | 26 June 2013, 17:25:44 UTC |
| a4cd5b1 | Feiyu Du | 26 June 2013, 16:06:47 UTC | fix the broken unit test | 26 June 2013, 16:06:47 UTC |
| 8047c3f | Feiyu Du | 26 June 2013, 15:15:10 UTC | change null gt from . to ./. | 26 June 2013, 15:16:43 UTC |
| e872b2c | Feiyu Du | 20 June 2013, 19:43:05 UTC | change not-available GT from . to ./. | 26 June 2013, 15:16:42 UTC |
| 5934562 | APipe Tester | 26 June 2013, 15:06:12 UTC | Updated `gmt` tab completion. | 26 June 2013, 15:06:12 UTC |
| 3280565 | APipe Tester | 26 June 2013, 15:05:27 UTC | Updated `genome` tab completion. | 26 June 2013, 15:05:27 UTC |
| 5e9f63e | APipe Tester | 26 June 2013, 15:03:55 UTC | Updated class browser cache. | 26 June 2013, 15:03:55 UTC |
| 42eb947 | Jasreet Hundal | 26 June 2013, 14:54:39 UTC | Tools to parse NetMHC3.4 online | 26 June 2013, 14:54:39 UTC |
| 9399c8c | Gabriel Sanderson | 25 June 2013, 23:45:35 UTC | Merge branch 'master' into gb_master | 25 June 2013, 23:45:35 UTC |
| 7192dee | Gabriel Sanderson | 25 June 2013, 23:36:29 UTC | Fixed bug that caused the REF to be included in ALT | 25 June 2013, 23:43:36 UTC |
| 50888ac | Travis Abbott | 25 June 2013, 23:02:47 UTC | bump vcf version, update test data this has to do with making sure gmt joinx normalize-indels uses natural vs numeric sorting | 25 June 2013, 23:02:47 UTC |
| a0d4444 | Travis Abbott | 25 June 2013, 22:24:04 UTC | use joinx sort instead of vcf-sort in indel normalization vcf-sort was sorting numerically (1,10,11,...) | 25 June 2013, 22:24:04 UTC |
| f76d311 | APipe Tester | 25 June 2013, 19:05:10 UTC | Updated `gmt` tab completion. | 25 June 2013, 19:05:10 UTC |
| 4157152 | APipe Tester | 25 June 2013, 19:03:40 UTC | Updated `genome` tab completion. | 25 June 2013, 19:03:40 UTC |
| 49cfe85 | APipe Tester | 25 June 2013, 19:00:00 UTC | Updated class browser cache. | 25 June 2013, 19:00:00 UTC |
| 4a84787 | Scott Smith | 25 June 2013, 18:41:39 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 June 2013, 18:41:39 UTC |
| 929093a | Scott Smith | 25 June 2013, 18:41:28 UTC | made DV2 BreakdancerMax.pm as a replacement for Breakdancer.pm, removing the hard-coded list of sequence names (1-22,X,Y) | 25 June 2013, 18:41:28 UTC |
| dcf5b58 | Adam Coffman | 25 June 2013, 18:38:56 UTC | add pooled rna as valid rna sample type | 25 June 2013, 18:38:56 UTC |
| 5f2f5f8 | APipe Tester | 25 June 2013, 17:48:55 UTC | Updated `gmt` tab completion. | 25 June 2013, 17:48:55 UTC |
| a6aede8 | APipe Tester | 25 June 2013, 17:48:06 UTC | Updated `genome` tab completion. | 25 June 2013, 17:48:06 UTC |
| ab0cb51 | APipe Tester | 25 June 2013, 17:46:30 UTC | Updated class browser cache. | 25 June 2013, 17:46:30 UTC |
| 70a4e0c | Malachi Griffith | 25 June 2013, 17:42:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 June 2013, 17:42:03 UTC |
| d4ec2a9 | Malachi Griffith | 25 June 2013, 17:41:48 UTC | Clinseq - handle rare edge case where prior clin-seq models were being identified as matching desired criteria even though PP of input models were not correct | 25 June 2013, 17:41:48 UTC |
| 2b8f025 | Chris Miller | 25 June 2013, 17:35:54 UTC | add sample name override, remove old tumor-only code | 25 June 2013, 17:36:09 UTC |
| ec5c008 | Chris Miller | 25 June 2013, 17:35:03 UTC | cleaning up tmp file | 25 June 2013, 17:36:08 UTC |
| 8663e5d | Scott Smith | 25 June 2013, 15:43:54 UTC | switch from Digest::SHA1 to Digest::SHA | 25 June 2013, 15:43:54 UTC |
| 10afb4d | Dave Larson | 25 June 2013, 15:20:07 UTC | This fix should ensure that, for a given gene/transcript pair, that the domains are always colored the same. This means that different mutation files for the same transcript should now show the same domain colors which was not always true before. | 25 June 2013, 15:20:07 UTC |
| 955abe3 | Ben Oberkfell | 24 June 2013, 21:16:40 UTC | Allocations cannot be archived if they are less than 1GB. Don't try to sweep up allocations smaller than that. | 24 June 2013, 22:10:54 UTC |
| b44138e | APipe Tester | 24 June 2013, 21:45:17 UTC | Updated `gmt` tab completion. | 24 June 2013, 21:45:48 UTC |
| beeacdd | APipe Tester | 24 June 2013, 21:43:56 UTC | Updated `genome` tab completion. | 24 June 2013, 21:45:48 UTC |
| dbd93ac | APipe Tester | 24 June 2013, 21:41:49 UTC | Updated class browser cache. | 24 June 2013, 21:45:48 UTC |
| b6fb6ab | Mark Burnett | 24 June 2013, 21:37:16 UTC | fix typo in debug message | 24 June 2013, 21:37:16 UTC |
| 436ba90 | Travis Abbott | 24 June 2013, 21:25:43 UTC | add breakdancer 1.4.1 | 24 June 2013, 21:25:43 UTC |
| 39f767b | Nathan Nutter | 24 June 2013, 16:19:04 UTC | add initial apipe-test-reference-alignment-lane-qc and sort | 24 June 2013, 16:19:21 UTC |
