| 4bd3109 | Chris Miller | 19 July 2013, 22:43:44 UTC | depth for 2+ bp deletions was calculated incorrectly | 19 July 2013, 22:43:44 UTC |
| 6301965 | Obi Griffith | 19 July 2013, 21:24:00 UTC | Added fix for old annotation formats with reversed start-stop | 19 July 2013, 21:24:00 UTC |
| 8169c40 | Eddie Belter | 18 July 2013, 22:21:12 UTC | Reconcile Misc Update: add status messages | 18 July 2013, 22:21:54 UTC |
| b0e0b0c | APipe Tester | 18 July 2013, 22:09:02 UTC | updated ur submodule to 84b8b16 | 18 July 2013, 22:09:02 UTC |
| 6af95b3 | APipe Tester | 18 July 2013, 21:44:33 UTC | updated ur submodule to 2279fc2 | 18 July 2013, 21:44:33 UTC |
| 43bd8a1 | Scott Smith | 18 July 2013, 21:29:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 July 2013, 21:29:15 UTC |
| 602970e | Scott Smith | 18 July 2013, 21:28:37 UTC | added GENOME_HOME environment variable | 18 July 2013, 21:28:37 UTC |
| d1d0c49 | APipe Tester | 18 July 2013, 21:22:52 UTC | Updated `gmt` tab completion. | 18 July 2013, 21:22:52 UTC |
| 72741bb | APipe Tester | 18 July 2013, 21:21:48 UTC | Updated `genome` tab completion. | 18 July 2013, 21:21:48 UTC |
| 0a4876c | APipe Tester | 18 July 2013, 21:19:31 UTC | Updated class browser cache. | 18 July 2013, 21:19:31 UTC |
| c13cd1d | Feiyu Du | 18 July 2013, 20:56:26 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 July 2013, 20:56:26 UTC |
| 13bd912 | Feiyu Du | 18 July 2013, 20:54:52 UTC | add required field platform:illumina into intermediate novo breakdancer config file | 18 July 2013, 20:54:52 UTC |
| 5dd8ff2 | Dave Larson | 18 July 2013, 20:37:52 UTC | increase requested memory from LSF for the Pindel job | 18 July 2013, 20:38:05 UTC |
| 93c81c3 | Ben Oberkfell | 18 July 2013, 20:13:06 UTC | GENOME_HOME was not an available enviroment variable | 18 July 2013, 20:13:06 UTC |
| 174b965 | Scott Smith | 18 July 2013, 19:18:38 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 July 2013, 19:18:38 UTC |
| f46c39c | Scott Smith | 18 July 2013, 19:18:02 UTC | updated model-group copy to take indirect params | 18 July 2013, 19:18:02 UTC |
| 093d783 | apregier | 18 July 2013, 15:53:52 UTC | Disconnect db handle during long-running assembly operations | 18 July 2013, 15:53:52 UTC |
| 7552503 | APipe Tester | 18 July 2013, 15:18:25 UTC | Updated `gmt` tab completion. | 18 July 2013, 15:18:25 UTC |
| 446fc74 | APipe Tester | 18 July 2013, 15:17:31 UTC | Updated `genome` tab completion. | 18 July 2013, 15:17:31 UTC |
| 6145c18 | APipe Tester | 18 July 2013, 15:15:43 UTC | Updated class browser cache. | 18 July 2013, 15:15:43 UTC |
| f0baef6 | Nathan Nutter | 18 July 2013, 14:45:54 UTC | Merge branch 'removal' | 18 July 2013, 15:06:17 UTC |
| 49e8778 | Nathan Nutter | 17 July 2013, 19:14:45 UTC | remove `gmt annotate genomic-regions` Command produces warnings when used and appears to have almost no usage: 2010/06/15 dkoboldt gmt annotate genomic-regions --help 2010/06/15 dkoboldt gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/06/02 ckandoth gmt annotate genomic-regions 2010/06/02 ckandoth gmt annotate genomic-regions --help 2010/06/02 ckandoth gmt annotate genomic-regions --help 2010/06/29 kchen gmt annotate genomic-regions 2010/06/30 wschierd gmt annotate genomic-regions --help 2010/06/30 wschierd gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/07/02 wschierd gmt annotate genomic-regions --help 2010/07/02 wschierd gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/07/02 wschierd gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/07/02 wschierd gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/08/11 jwalker gmt annotate genomic-regions --help 2010/08/11 jwalker gmt annotate genomic-regions --help 2011/01/12 jwallis gmt annotate genomic-regions --help 2012/07/24 dmorton gmt annotate genomic-regions --help 2013/07/10 jhundal gmt annotate genomic-regions --help | 18 July 2013, 15:06:15 UTC |
| 14077cd | Nathan Nutter | 16 July 2013, 19:12:43 UTC | remove unused/old code We believe these were either never really used or were only used experimentally so we are removing the code and archiving the database data. If one of these turns out to be needed then contact APIPE to coordinate a restore. Related classes: Genome::Disease Genome::Model::BuildSV Genome::Model::SV Genome::Model::VariantSource Genome::Model::VariantValidation Genome::SNVManualReview Genome::SequenceDiff Genome::SequenceDiffEval Genome::SequenceDiffPart Genome::UpdateHistory Genome::VRList Genome::VRListMember Genome::VariantOccurrence Genome::VariantReviewDetail Genome::VariantReviewDetailOld Genome::VariantReviewList Genome::VariantReviewListFilter Genome::VariantReviewListMember Related tables: DISEASE GENOME_MODEL_BUILD_SV GENOME_MODEL_SV GENOME_MODEL_VARIANT_SOURCE GENOME_MODEL_VARIANTVALIDATION SNV_MANUAL_REVIEW SEQUENCE_DIFF SEQUENCE_DIFF_EVAL SEQUENCE_DIFF_PART GENOME_VR_LIST GENOME_VR_LIST_MEMBER VARIANT_OCCURRENCE VARIANT_REVIEW_DETAIL VARIANT_REVIEW_DETAIL_OLD VARIANT_REVIEW_LIST VARIANT_REVIEW_LIST_FILTER VARIANT_REVIEW_LIST_MEMBER | 18 July 2013, 15:06:13 UTC |
| a51290d | Jim Weible | 18 July 2013, 14:38:39 UTC | skip generate merged assemblies if we don't have a merged fasta file | 18 July 2013, 14:38:39 UTC |
| 8d341e1 | Scott Smith | 17 July 2013, 19:05:03 UTC | add GENOME_HOME to Site::TGI | 17 July 2013, 19:05:03 UTC |
| c5cfb29 | Scott Smith | 17 July 2013, 18:43:00 UTC | "genome model export metadata" code and test | 17 July 2013, 18:43:00 UTC |
| e9d51d3 | APipe Tester | 17 July 2013, 18:37:22 UTC | Updated `gmt` tab completion. | 17 July 2013, 18:37:22 UTC |
| 232127d | APipe Tester | 17 July 2013, 18:36:27 UTC | Updated `genome` tab completion. | 17 July 2013, 18:36:27 UTC |
| 1255d4d | APipe Tester | 17 July 2013, 18:33:42 UTC | Updated class browser cache. | 17 July 2013, 18:33:42 UTC |
| 5814856 | Jasreet Hundal | 17 July 2013, 18:21:06 UTC | Renaming module | 17 July 2013, 18:21:06 UTC |
| 57fe376 | apregier | 17 July 2013, 17:27:01 UTC | Merge branch 'generator' into gb_master | 17 July 2013, 17:27:01 UTC |
| f1fd599 | apregier | 11 July 2013, 15:07:54 UTC | Move CreateMutationDiagrams off of db | 17 July 2013, 17:23:52 UTC |
| e32e9c1 | apregier | 10 July 2013, 21:50:40 UTC | Add a way to pass in data directories for somatic variation and annotation builds | 17 July 2013, 17:18:39 UTC |
| 1abfb82 | Thomas Mooney | 17 July 2013, 15:26:04 UTC | This...is...Pindel. | 17 July 2013, 15:26:04 UTC |
| b5ebfe1 | Veena Bhonagiri | 17 July 2013, 15:08:03 UTC | removed version numbers from pipeline email | 17 July 2013, 15:08:03 UTC |
| 60b3779 | APipe Tester | 16 July 2013, 19:26:54 UTC | Updated `gmt` tab completion. | 16 July 2013, 19:26:54 UTC |
| e5cb5c6 | APipe Tester | 16 July 2013, 19:25:58 UTC | Updated `genome` tab completion. | 16 July 2013, 19:25:58 UTC |
| 2de02f2 | APipe Tester | 16 July 2013, 19:23:49 UTC | Updated class browser cache. | 16 July 2013, 19:23:49 UTC |
| 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 |
| 391d85d | Scott Smith | 16 July 2013, 15:37:19 UTC | Mexport erge branch 'master' of ssh://git/srv/git/genome | 16 July 2013, 15:37:19 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 |
| fe4c0a7 | Scott Smith | 16 July 2013, 00:06:16 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 July 2013, 00:06:16 UTC |
| a1017c7 | Scott Smith | 16 July 2013, 00:04:40 UTC | Default GENOME_SYS_ID for TGI to 'GMS1' | 16 July 2013, 00:04:40 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 |
