| 41ad296 | Gabriel Sanderson | 05 August 2014, 22:08:55 UTC | updated mentions of joinx1.8 to 1.9 in test cases | 05 August 2014, 22:08:55 UTC |
| 6835e7a | Gabriel Sanderson | 05 August 2014, 20:46:58 UTC | update plans to use joinx 1.9 | 05 August 2014, 20:46:58 UTC |
| 06cf7ea | Gabriel Sanderson | 05 August 2014, 20:27:13 UTC | update default joinx version to 1.9 | 05 August 2014, 20:27:33 UTC |
| 5cc0b5c | Susanna Siebert | 05 August 2014, 19:32:49 UTC | Eval the call to Genome::Sys->rename Genome::Sys->rename will die if it fails which will prevent the callback from working and retrying. | 05 August 2014, 19:43:43 UTC |
| f057f05 | apregier | 05 August 2014, 19:36:40 UTC | Merge branch 'copy' into gb_master | 05 August 2014, 19:36:40 UTC |
| 0e88a4d | apregier | 05 August 2014, 19:05:15 UTC | Skip entries with messed up CAF entries - they will simply not be counted toward the af_count metric | 05 August 2014, 19:34:34 UTC |
| 032ba1c | Adam Coffman | 05 August 2014, 17:50:04 UTC | make lack of lq variants in tiering non-fatal | 05 August 2014, 17:50:04 UTC |
| a162e4c | Thomas Mooney | 05 August 2014, 15:50:00 UTC | Use a raw SQL query to efficiently populate this view. The old version was taking > 3000sec and 3 GB of memory, so this will get us by in the meanwhile. | 05 August 2014, 15:50:00 UTC |
| 2651720 | Thomas Mooney | 05 August 2014, 13:32:25 UTC | New classes to define tags and to link them to profile items. | 05 August 2014, 13:32:25 UTC |
| e7dab07 | Thomas Mooney | 05 August 2014, 13:01:25 UTC | More efficient query for the count in the model-group display name. | 05 August 2014, 13:01:25 UTC |
| 6fa6045 | Thomas Mooney | 04 August 2014, 22:25:17 UTC | Tables to support tagging of configurations in AnP Config | 04 August 2014, 22:25:17 UTC |
| f006645 | Gabriel Sanderson | 01 August 2014, 22:08:48 UTC | Handle alt_bases_for_sample and genotype_for_sample returning undef. | 01 August 2014, 22:16:06 UTC |
| 82fba5d | Gabriel Sanderson | 01 August 2014, 22:15:28 UTC | alt_bases_for_sample returns undef if no genotype found. | 01 August 2014, 22:16:05 UTC |
| 9375120 | Gabriel Sanderson | 01 August 2014, 21:15:46 UTC | Correct bug in File::Vcf::Entry. Change behavior when no sample present. File::Vcf::Entry contained a bug where the bounds of the sample index was too permissive by 1. We also now return undef instead of confessing when we have no GT information for a sample - the sample might just be '.'. Corrected an oversight in the unit test - there were not enough samples in the header for the "get genotype for sample" subtest data. And we had to correct the behavior assumptions when dying for the above. | 01 August 2014, 21:19:43 UTC |
| 1f15b9b | Feiyu Du | 01 August 2014, 21:07:17 UTC | renamed | 01 August 2014, 21:07:17 UTC |
| 49cc615 | dmorton | 01 August 2014, 20:32:36 UTC | Clean up HeaderDiff->print output for sample name diffs | 01 August 2014, 20:33:20 UTC |
| 60c9979 | Feiyu Du | 01 August 2014, 20:17:32 UTC | add vep MaxSegdupFilter | 01 August 2014, 20:17:32 UTC |
| 1a4ffb9 | apregier | 01 August 2014, 17:24:01 UTC | Merge branch 'updated' into gb_master | 01 August 2014, 17:24:01 UTC |
| 71c8fea | apregier | 01 August 2014, 16:10:06 UTC | Run reports with d30 model as base | 01 August 2014, 17:20:34 UTC |
| ebf3fa8 | apregier | 01 August 2014, 15:32:06 UTC | Use network file location for intermediate output file | 01 August 2014, 15:32:47 UTC |
| 82fdc6e | APipe Tester | 01 August 2014, 12:18:09 UTC | Updated `gmt` tab completion. | 01 August 2014, 12:18:09 UTC |
| 6713a21 | APipe Tester | 01 August 2014, 12:17:28 UTC | Updated `genome` tab completion. | 01 August 2014, 12:17:28 UTC |
| 81e9255 | APipe Tester | 01 August 2014, 12:15:39 UTC | Updated class browser cache. | 01 August 2014, 12:15:39 UTC |
| e55e803 | APipe Tester | 31 July 2014, 21:47:56 UTC | updated ur submodule to f5acb4c | 31 July 2014, 21:47:56 UTC |
| cc72c98 | apregier | 31 July 2014, 21:33:57 UTC | Merge branch 'fireteam' into gb_master | 31 July 2014, 21:33:57 UTC |
| 90fa80e | apregier | 31 July 2014, 21:31:11 UTC | Change annotate-with-readcount to take sample name This way, the tool can add an additional sample name if it doesn't already exist in the vcf file. | 31 July 2014, 21:31:11 UTC |
| 4fe08f8 | apregier | 31 July 2014, 18:47:14 UTC | Don't separately add sample name to input vcfs | 31 July 2014, 21:23:46 UTC |
| 875ac9c | Ian Ferguson | 31 July 2014, 20:44:13 UTC | Fix Cufflinks memory request during testing | 31 July 2014, 20:44:40 UTC |
| e6177d8 | Eddie Belter | 31 July 2014, 19:26:33 UTC | GMT: add gatk command tree class | 31 July 2014, 19:26:33 UTC |
| d369197 | Eddie Belter | 31 July 2014, 19:14:34 UTC | DV2: use full GATK class name to check legacy version | 31 July 2014, 19:14:34 UTC |
| 3eefca4 | apregier | 31 July 2014, 18:55:24 UTC | Merge branch 'updated' into gb_master | 31 July 2014, 18:55:24 UTC |
| f7c54fe | apregier | 30 July 2014, 17:47:56 UTC | Fix pindel sorting | 31 July 2014, 18:54:17 UTC |
| 44fd477 | Eddie Belter | 30 July 2014, 23:51:31 UTC | InstData Gatk: add -n to rusage in refine reads gatk base | 31 July 2014, 17:42:39 UTC |
| 20e31d0 | Eddie Belter | 30 July 2014, 23:47:32 UTC | InstData Gatk: update threading in indel realigner | 31 July 2014, 17:42:39 UTC |
| f69b696 | Eddie Belter | 30 July 2014, 23:44:18 UTC | InstData Gatk: specify rusage for best practices commands | 31 July 2014, 17:42:38 UTC |
| fe35a5c | Eddie Belter | 30 July 2014, 23:33:35 UTC | InstData GATK: max memory returns GB | 31 July 2014, 17:42:38 UTC |
| 706a6e6 | Eddie Belter | 15 July 2014, 17:50:44 UTC | InstData GATK: do not compare grp output from base recalibrator test | 31 July 2014, 17:42:37 UTC |
| 3e5f53d | Eddie Belter | 15 July 2014, 17:08:41 UTC | InstData GATK: set max_memory for gatk tools using Genome::Sys | 31 July 2014, 17:42:37 UTC |
| 46f1431 | Eddie Belter | 14 July 2014, 22:37:18 UTC | InstData GATK: use threading | 31 July 2014, 17:42:36 UTC |
| bbbc619 | Eddie Belter | 14 July 2014, 19:36:43 UTC | GMT GATK: use threading mix in classes as appropriate | 31 July 2014, 17:42:36 UTC |
| 8bf40bc | Eddie Belter | 14 July 2014, 19:35:27 UTC | GMT GATK: add mix in classes for threading options | 31 July 2014, 17:42:35 UTC |
| 7bb0c15 | Eddie Belter | 10 July 2014, 20:06:24 UTC | Gatk: rename the base class | 31 July 2014, 17:42:35 UTC |
| c792695 | Thomas Mooney | 31 July 2014, 13:13:17 UTC | Consistently use the build's assigned instrument data. The model's assignments may have changed (or be nonexistent!) | 31 July 2014, 13:13:46 UTC |
| 8e42bb8 | APipe Tester | 31 July 2014, 12:17:11 UTC | Updated `gmt` tab completion. | 31 July 2014, 12:17:11 UTC |
| 5dd4d4e | APipe Tester | 31 July 2014, 12:16:31 UTC | Updated `genome` tab completion. | 31 July 2014, 12:16:31 UTC |
| 942c5d0 | APipe Tester | 31 July 2014, 12:15:10 UTC | Updated class browser cache. | 31 July 2014, 12:15:10 UTC |
| 8662a4a | kmeltzst | 30 July 2014, 21:06:16 UTC | memoize bam index | 30 July 2014, 21:06:47 UTC |
| 36c8e6c | Feiyu Du | 30 July 2014, 20:55:18 UTC | update ref-align test build | 30 July 2014, 20:55:18 UTC |
| 29dc76f | kmeltzst | 30 July 2014, 20:50:13 UTC | don't make bam.index hardcoded | 30 July 2014, 20:50:13 UTC |
| 1c166df | Susanna Siebert | 30 July 2014, 18:07:14 UTC | ensure that skipping of loh is handled conistently between steps | 30 July 2014, 18:34:42 UTC |
| 68cb1c6 | Feiyu Du | 30 July 2014, 18:33:45 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 30 July 2014, 18:33:45 UTC |
| f61b3e3 | Feiyu Du | 30 July 2014, 18:33:36 UTC | md5 update | 30 July 2014, 18:33:36 UTC |
| 4246703 | Adam Coffman | 30 July 2014, 18:19:10 UTC | make wingspan optional | 30 July 2014, 18:19:10 UTC |
| 75736ab | Feiyu Du | 30 July 2014, 16:46:42 UTC | remove -a | 30 July 2014, 16:46:42 UTC |
| 18d2388 | Thomas Mooney | 30 July 2014, 13:47:04 UTC | Turn `genome analysis-project show-config` into a lister. | 30 July 2014, 13:47:04 UTC |
| caca761 | Thomas Mooney | 29 July 2014, 21:18:51 UTC | Display notice when an Analysis Project is Pending. | 29 July 2014, 21:18:51 UTC |
| 21f719e | Thomas Mooney | 29 July 2014, 21:15:25 UTC | Default test Analysis Projects to "In Progress". | 29 July 2014, 21:15:25 UTC |
| 2c5f314 | Thomas Mooney | 29 July 2014, 21:06:55 UTC | Don't process a new Analysis Project until it is explicitly released. | 29 July 2014, 21:06:55 UTC |
| 189c3c2 | Nathaniel Nutter | 25 July 2014, 18:06:03 UTC | avoid loading all models just to get count | 29 July 2014, 19:51:27 UTC |
| 6cb1628 | Nathaniel Nutter | 22 July 2014, 18:59:22 UTC | ModelGroup will unload its bridge objects | 29 July 2014, 19:51:25 UTC |
| 3f61366 | apregier | 29 July 2014, 18:51:25 UTC | Merge branch 'fireteam' into gb_master | 29 July 2014, 18:51:25 UTC |
| e684cb1 | apregier | 29 July 2014, 18:48:13 UTC | ignore gitignore files, that need to be there so the directories stay | 29 July 2014, 18:48:13 UTC |
| fd07eef | apregier | 29 July 2014, 18:37:11 UTC | Merge branch 'fireteam' into gb_master | 29 July 2014, 18:37:11 UTC |
| ebd1c3d | apregier | 29 July 2014, 18:35:54 UTC | Add directories to repo | 29 July 2014, 18:35:54 UTC |
| 1b1bea7 | apregier | 29 July 2014, 18:15:33 UTC | Merge branch 'fireteam' into gb_master | 29 July 2014, 18:15:33 UTC |
| 7c8c23b | apregier | 29 July 2014, 18:13:33 UTC | Only compare existance of files, not content | 29 July 2014, 18:13:33 UTC |
| feaf4f6 | apregier | 29 July 2014, 17:24:43 UTC | Merge branch 'fireteam' into gb_master | 29 July 2014, 17:24:43 UTC |
| cfacb40 | apregier | 28 July 2014, 22:04:19 UTC | Compare output directories in wrapper test | 29 July 2014, 17:24:12 UTC |
| 9b2b5b3 | apregier | 28 July 2014, 22:03:57 UTC | Skip log directories during file comparisons | 29 July 2014, 16:57:27 UTC |
| c90fdc5 | apregier | 28 July 2014, 21:25:39 UTC | Move compare_directories into test helper | 29 July 2014, 16:57:27 UTC |
| f10c48a | apregier | 28 July 2014, 21:21:09 UTC | Add test for running reports starting with wrapper | 29 July 2014, 16:57:26 UTC |
| 0ff30e6 | apregier | 28 July 2014, 21:19:45 UTC | Move build creation to test helper | 29 July 2014, 16:57:25 UTC |
| 11ef056 | apregier | 28 July 2014, 19:28:50 UTC | Change to debug message | 29 July 2014, 16:57:25 UTC |
| fabceec | Thomas Mooney | 29 July 2014, 14:26:50 UTC | Also return if genome_length came back 0 to avoid dividing by it. | 29 July 2014, 14:26:50 UTC |
| d39e1bc | Thomas Mooney | 28 July 2014, 22:34:55 UTC | Remove import of "mode" subroutine from modules no longer using it. | 28 July 2014, 22:34:55 UTC |
| 8b4576d | Avinash Ramu | 28 July 2014, 21:57:01 UTC | revert until test-factory issue is resolved | 28 July 2014, 21:57:01 UTC |
| 6454408 | Malachi Griffith | 28 July 2014, 21:17:33 UTC | update clin-seq default to latest version of cosmic annotation db that has the latest annotations from Ensembl | 28 July 2014, 21:17:33 UTC |
| 8e5da35 | apregier | 28 July 2014, 19:25:45 UTC | Merge branch 'fireteam' into gb_master | 28 July 2014, 19:25:45 UTC |
| a230115 | apregier | 28 July 2014, 19:05:41 UTC | Revert "catch create exceptions within get_or_create" This reverts commit efc605b1f6a821b3f737ded8fe43e9ff3df7aa2d. | 28 July 2014, 19:06:18 UTC |
| dc594d8 | apregier | 28 July 2014, 19:04:42 UTC | Revert "can't propogate exception or something swallows it" This reverts commit 8223e0899bae5d572647e16c71d7f703f66bd2fc. | 28 July 2014, 19:06:18 UTC |
| 5c3fcb4 | Nathaniel Nutter | 28 July 2014, 18:04:32 UTC | fix issues for RT/100194 - only generate IGV XML files for known references - get tier bed path from Tier result | 28 July 2014, 18:04:32 UTC |
| 1552189 | Nathaniel Nutter | 25 July 2014, 21:19:12 UTC | only generate IGV XML files for known references | 28 July 2014, 17:49:37 UTC |
| 76eaccb | Nathaniel Nutter | 23 July 2014, 22:43:29 UTC | get tier bed path from Tier result | 28 July 2014, 17:49:36 UTC |
| cf8d1a8 | Nathaniel Nutter | 23 July 2014, 22:41:44 UTC | add option to filter results from glob on pattern Maintains support for glob pattern but allows flexibility when needed. | 28 July 2014, 17:49:34 UTC |
| 51cf314 | Nathaniel Nutter | 23 July 2014, 22:40:24 UTC | croak instead of die It's a non-unique pattern which caused the failure so die from caller's perspective (croak). | 28 July 2014, 17:49:32 UTC |
| 9721a52 | APipe Tester | 25 July 2014, 22:35:43 UTC | updated ur submodule to 148d9a2 | 25 July 2014, 22:35:43 UTC |
| 162f89d | Gabriel Sanderson | 25 July 2014, 21:06:38 UTC | Respect GENOME_SOFTWARE_RESULT_TEST_NAME | 25 July 2014, 21:06:45 UTC |
| fc524a7 | Tiandao Li | 25 July 2014, 19:48:12 UTC | model IDs | 25 July 2014, 19:48:12 UTC |
| 82bc726 | Eddie Belter | 25 July 2014, 18:37:51 UTC | InstData Import: basic uses work flow helpers | 25 July 2014, 18:37:51 UTC |
| ec9c7f2 | Eddie Belter | 25 July 2014, 18:15:23 UTC | GMT GeneTorrent: calculate rate limit from lsf rusage | 25 July 2014, 18:15:23 UTC |
| a8b355f | Eddie Belter | 25 July 2014, 16:54:21 UTC | Helpers: add workflow building | 25 July 2014, 16:54:21 UTC |
| 842432a | dmorton | 25 July 2014, 03:03:55 UTC | Don't memoize something that is only called once | 25 July 2014, 03:04:44 UTC |
| 0e44296 | dmorton | 25 July 2014, 03:03:39 UTC | Use differ instead of compare_ok | 25 July 2014, 03:04:43 UTC |
| c1ae14c | dmorton | 25 July 2014, 03:03:00 UTC | Avoid is_many lookups (they're very slow) | 25 July 2014, 03:04:43 UTC |
| cb56939 | dmorton | 25 July 2014, 03:02:35 UTC | Make decode and encode even faster | 25 July 2014, 03:04:43 UTC |
| 7aad445 | dmorton | 25 July 2014, 01:15:10 UTC | Change way that BamReadcount::Entry en(de)codes for vcf | 25 July 2014, 03:04:43 UTC |
| ba26fb7 | dmorton | 24 July 2014, 20:49:50 UTC | use get_class instead of _load | 25 July 2014, 03:04:43 UTC |
| ffc430e | dmorton | 24 July 2014, 20:49:33 UTC | Make factory a package global in plan base class | 25 July 2014, 03:04:43 UTC |
| 75fd898 | dmorton | 24 July 2014, 20:49:00 UTC | stop calling _load more than once | 25 July 2014, 03:04:43 UTC |
| f351889 | dmorton | 24 July 2014, 20:48:13 UTC | Do not report on or try to interpret when all alts are failed | 25 July 2014, 03:04:43 UTC |
