| b19d08f | Thomas B. Mooney | 21 April 2015, 14:43:39 UTC | Merge pull request #668 from tmooney/allow_assumed_variant_status_in_simplify_vcf SimplifyVCF: Add option to declare all unfiltered variants as passing/failing. | 21 April 2015, 14:43:39 UTC |
| 7bd4056 | APipe Tester | 21 April 2015, 12:51:39 UTC | Updated `gmt` tab completion. | 21 April 2015, 12:51:39 UTC |
| c092d71 | APipe Tester | 21 April 2015, 12:50:54 UTC | Updated `genome` tab completion. | 21 April 2015, 12:50:54 UTC |
| 7cb08b7 | APipe Tester | 21 April 2015, 12:49:02 UTC | Updated class browser cache. | 21 April 2015, 12:49:02 UTC |
| ebac3c4 | Thomas B. Mooney | 20 April 2015, 19:53:12 UTC | Merge pull request #671 from tmooney/update_anp_add_docs Create common base class and update docs for AnP config-adding commands | 20 April 2015, 19:53:12 UTC |
| 6120ad0 | Thomas B. Mooney | 20 April 2015, 19:38:24 UTC | Merge pull request #646 from tmooney/find_potentially_matching_references New command to find references that have the same chromosome names as a query file. | 20 April 2015, 19:38:24 UTC |
| f7c4b23 | Thomas Mooney | 09 April 2015, 13:43:04 UTC | Use new don't-create option instead of inspecting build directly. | 20 April 2015, 18:15:48 UTC |
| a6dfe97 | Thomas Mooney | 09 April 2015, 13:42:33 UTC | Use File::Spec. | 20 April 2015, 18:15:48 UTC |
| 98f8bfe | Thomas Mooney | 09 April 2015, 13:41:59 UTC | Optionally don't try to auto-create sequence dictionary. | 20 April 2015, 18:15:48 UTC |
| e016d18 | Thomas Mooney | 08 April 2015, 21:36:21 UTC | New command to find references we're not sure aren't related to a file. We can be sure some aren't related, but we cannot know if the returned references have anything to do with the file or not. | 20 April 2015, 18:10:32 UTC |
| d25ee50 | Indraniel | 20 April 2015, 16:51:30 UTC | Merge pull request #640 from indraniel/vcf-evaluate GMT Integration of VCF Evaluation (part 1) | 20 April 2015, 16:51:30 UTC |
| eb6cd75 | Avinash Ramu | 20 April 2015, 15:58:28 UTC | Merge pull request #628 from gatoravi/clinseq_add_loh Module to identify LOH regions. | 20 April 2015, 15:58:28 UTC |
| 75079f3 | Avinash Ramu | 20 April 2015, 15:35:55 UTC | glob before unlink | 20 April 2015, 15:35:55 UTC |
| 1e1cde8 | Susanna Siebert | 20 April 2015, 15:06:23 UTC | Merge pull request #672 from susannasiebert/variant_reporting_docm Add gene annotations to the DoCM report and remove the trio.t test | 20 April 2015, 15:06:23 UTC |
| 14e11ff | Susanna Siebert | 20 April 2015, 14:46:22 UTC | Reword error message | 20 April 2015, 14:46:22 UTC |
| b999029 | Thomas Mooney | 20 April 2015, 13:56:00 UTC | Double-check that the profile item wasn't there already. | 20 April 2015, 13:56:00 UTC |
| c1119ec | Thomas Mooney | 20 April 2015, 13:52:56 UTC | Add stub for _create_profile_items. | 20 April 2015, 13:52:56 UTC |
| bf93137 | Thomas B. Mooney | 20 April 2015, 13:47:57 UTC | Merge pull request #669 from tmooney/failx_isnt_a_thing ReferenceSequence Build: Fix typos and remove trailing whitespace. | 20 April 2015, 13:47:57 UTC |
| 0efe615 | Thomas B. Mooney | 20 April 2015, 13:47:26 UTC | Merge pull request #670 from tmooney/availble_quiting Fix more typos. | 20 April 2015, 13:47:26 UTC |
| 8d8f027 | APipe Tester | 20 April 2015, 12:43:32 UTC | updated workflow submodule to 2d658c9 | 20 April 2015, 12:43:32 UTC |
| 0d2d195 | APipe Tester | 18 April 2015, 12:17:05 UTC | Updated `gmt` tab completion. | 18 April 2015, 12:17:05 UTC |
| 63be564 | APipe Tester | 18 April 2015, 12:16:19 UTC | Updated `genome` tab completion. | 18 April 2015, 12:16:19 UTC |
| 3d3bbf6 | APipe Tester | 18 April 2015, 12:14:41 UTC | Updated class browser cache. | 18 April 2015, 12:14:41 UTC |
| bafc5be | Feiyu Du | 17 April 2015, 22:05:59 UTC | Merge pull request #675 from dufeiyu/bug_fix Bug fix: bam_file, not get_bam_file | 17 April 2015, 22:05:59 UTC |
| 017a98f | Feiyu Du | 17 April 2015, 20:07:22 UTC | bug fix get_bam_file -> bam_file | 17 April 2015, 20:07:22 UTC |
| b888c88 | Avinash Ramu | 17 April 2015, 17:19:54 UTC | update docs | 17 April 2015, 17:19:54 UTC |
| 5af7f3b | Nathaniel Nutter | 17 April 2015, 17:15:51 UTC | Merge pull request #674 from nnutter/master fix test failure on master due to missing use | 17 April 2015, 17:15:51 UTC |
| d7619b5 | Nathaniel Nutter | 17 April 2015, 16:45:02 UTC | fix test failure on master due to missing use | 17 April 2015, 16:45:02 UTC |
| 6b33ed1 | Avinash Ramu | 17 April 2015, 16:22:25 UTC | specify version in test. | 17 April 2015, 16:22:25 UTC |
| 4860108 | Avinash Ramu | 17 April 2015, 16:05:20 UTC | make bamrc configurable | 17 April 2015, 16:05:20 UTC |
| 9cfa3d5 | mkiwala | 17 April 2015, 15:58:49 UTC | Merge pull request #643 from davidlmorton/ptero-integration-improvements Ptero integration improvements | 17 April 2015, 15:58:49 UTC |
| 52dad2e | Susanna Siebert | 17 April 2015, 15:39:41 UTC | Add version check for allow_same_file option to Joinx::VcfMerge | 17 April 2015, 15:39:41 UTC |
| 234df33 | Feiyu Du | 17 April 2015, 15:32:05 UTC | Merge pull request #663 from dufeiyu/get_bam_file A new method get_bam_file to handle lock and return revivified bam or copied in-place bam | 17 April 2015, 15:32:05 UTC |
| d6ff526 | Gue Su Chang | 17 April 2015, 15:18:10 UTC | Merge pull request #673 from gschang/master Fixation of the test error in Genome::Model::Tools::Analysis::Coverage::... Since there was only a simple change in the test script, I made this merge quickly. | 17 April 2015, 15:18:10 UTC |
| f9314fe | Gue Su Chang | 17 April 2015, 15:15:19 UTC | Fixation of the test error in Genome::Model::Tools::Analysis::Coverage::MergeReadcounts | 17 April 2015, 15:15:19 UTC |
| 773d014 | Avinash Ramu | 17 April 2015, 15:04:54 UTC | make bamrc version configurable | 17 April 2015, 15:04:54 UTC |
| aaf46d9 | Susanna Siebert | 17 April 2015, 15:04:10 UTC | Update blessed trio_main process | 17 April 2015, 15:04:10 UTC |
| 8b074c9 | Susanna Siebert | 15 April 2015, 20:21:20 UTC | Remove trio test | 17 April 2015, 14:52:10 UTC |
| c3a73fe | Susanna Siebert | 11 March 2015, 20:45:58 UTC | add new short_name option | 17 April 2015, 14:52:10 UTC |
| e209ab2 | Susanna Siebert | 09 March 2015, 19:37:34 UTC | Have the docm report use joinx 1.11 with allow-same-file option | 17 April 2015, 14:52:09 UTC |
| c1c6192 | Susanna Siebert | 09 March 2015, 19:31:42 UTC | Add support for joinx 1.11 allow-same-file option to vep expert | 17 April 2015, 14:52:09 UTC |
| 43184a8 | Susanna Siebert | 09 March 2015, 19:29:50 UTC | Add support for joinx 1.11 allow-same-file option | 17 April 2015, 14:52:09 UTC |
| 418ec9b | Susanna Siebert | 22 January 2015, 18:59:14 UTC | add vep annotations to the DoCM report | 17 April 2015, 14:52:09 UTC |
| 7ad2793 | Susanna Siebert | 17 April 2015, 14:51:46 UTC | Merge pull request #588 from susannasiebert/process_comparison Handle symlink comparison more explicitly when comparing process output | 17 April 2015, 14:51:46 UTC |
| 86c0b53 | Gue Su Chang | 17 April 2015, 14:34:37 UTC | Merge pull request #664 from gschang/master Upgrade in Genome::Model::Tools::Analysis::Coverage::MergeReadcounts and... | 17 April 2015, 14:34:37 UTC |
| 7ed57eb | APipe Tester | 17 April 2015, 12:39:41 UTC | Updated `gmt` tab completion. | 17 April 2015, 12:39:41 UTC |
| f9d80c1 | APipe Tester | 17 April 2015, 12:38:55 UTC | Updated `genome` tab completion. | 17 April 2015, 12:38:55 UTC |
| 61ecd92 | APipe Tester | 17 April 2015, 07:25:45 UTC | updated ur submodule to d1536b9 | 17 April 2015, 08:28:13 UTC |
| f044a8e | Nathaniel Nutter | 17 April 2015, 08:17:53 UTC | Merge pull request #667 from nnutter/tgisan remove 'unknown' and 'tgisan' lock scopes | 17 April 2015, 08:17:53 UTC |
| 6d6d4c8 | Thomas Mooney | 16 April 2015, 22:50:04 UTC | Deduplicate valid_statuses by being more careful when to preprocess. | 16 April 2015, 22:53:36 UTC |
| 8a4d744 | Thomas Mooney | 16 April 2015, 22:49:27 UTC | add-config-file no longer returns the new profile item. | 16 April 2015, 22:49:27 UTC |
| c8c5dab | Thomas Mooney | 16 April 2015, 22:46:39 UTC | Whitespace. | 16 April 2015, 22:46:39 UTC |
| 90c54dc | Thomas Mooney | 16 April 2015, 22:37:08 UTC | Add newline to end of synopsis section. | 16 April 2015, 22:37:08 UTC |
| fa6851d | Thomas Mooney | 16 April 2015, 22:35:17 UTC | Base class for adding configuration to an AnalysisProject. | 16 April 2015, 22:35:17 UTC |
| 8d5c15b | Thomas Mooney | 16 April 2015, 22:08:31 UTC | Update detailed help. * More clear explanation of what the command does. * Mention option for interactive use. * Mention "add-config-file" for custom configs. | 16 April 2015, 22:08:31 UTC |
| 8861c0e | Thomas Mooney | 16 April 2015, 22:04:34 UTC | Synopsis of correct command. | 16 April 2015, 22:06:14 UTC |
| 32ee3fc | Thomas Mooney | 16 April 2015, 22:02:01 UTC | Easier to understand detail text, and refer to other add command. | 16 April 2015, 22:02:01 UTC |
| c4fe94a | Thomas Mooney | 16 April 2015, 22:01:34 UTC | Make documentation more similar to "add-menu-item". | 16 April 2015, 22:01:34 UTC |
| 73cd7a3 | Thomas Mooney | 16 April 2015, 21:46:57 UTC | Repunctuate doc line. | 16 April 2015, 21:46:57 UTC |
| 4fe4acf | Thomas Mooney | 16 April 2015, 21:46:30 UTC | Remove redundant display of default. | 16 April 2015, 21:46:30 UTC |
| 03dbf2e | Thomas Mooney | 16 April 2015, 21:45:01 UTC | Remove extra "-config" from synopsis. | 16 April 2015, 21:45:01 UTC |
| e7ff08c | Thomas Mooney | 16 April 2015, 21:08:55 UTC | Typo: quiting => quitting | 16 April 2015, 21:08:55 UTC |
| 301f5bc | Thomas Mooney | 16 April 2015, 21:05:12 UTC | Typo: quiting => quitting | 16 April 2015, 21:05:12 UTC |
| 4bb8e81 | Thomas Mooney | 16 April 2015, 21:02:51 UTC | Typo: availble => available | 16 April 2015, 21:02:51 UTC |
| 54cac5a | Avinash Ramu | 16 April 2015, 20:58:19 UTC | check for empty data-frame better | 16 April 2015, 20:58:19 UTC |
| 5f53cd9 | Thomas Mooney | 16 April 2015, 20:55:55 UTC | Typo: availble => available | 16 April 2015, 20:55:55 UTC |
| 5a87048 | Thomas Mooney | 16 April 2015, 20:53:36 UTC | Typo: quiting => quitting. | 16 April 2015, 20:54:40 UTC |
| 8fd9d75 | Thomas Mooney | 16 April 2015, 20:49:18 UTC | Remove trailing whitespace. | 16 April 2015, 20:49:18 UTC |
| 6887a73 | Thomas Mooney | 16 April 2015, 20:48:41 UTC | Fix typo: failx => faidx. | 16 April 2015, 20:48:41 UTC |
| 633a292 | Gue Su Chang | 16 April 2015, 20:46:06 UTC | Test for Genome::Model::Tools::Analysis::Coverage::MergeReadcounts | 16 April 2015, 20:46:06 UTC |
| c94e2ff | Thomas Mooney | 16 April 2015, 20:32:33 UTC | Remove breakpoint. | 16 April 2015, 20:32:33 UTC |
| cd06622 | Thomas Mooney | 16 April 2015, 20:31:58 UTC | Whitespace. * Remove trailing whitespace. * Consistently use four-space indent. | 16 April 2015, 20:31:58 UTC |
| a8d9838 | Thomas Mooney | 16 April 2015, 20:23:08 UTC | Use warning message instead of printing. | 16 April 2015, 20:24:05 UTC |
| d53f489 | Avinash Ramu | 16 April 2015, 20:20:39 UTC | fix filtering param. | 16 April 2015, 20:20:39 UTC |
| 546e4aa | Avinash Ramu | 16 April 2015, 20:19:41 UTC | don't stop at first empty chr. There might be chromosomes down the line with data. | 16 April 2015, 20:19:41 UTC |
| b861c3e | Thomas Mooney | 16 April 2015, 19:26:31 UTC | Add option to declare all unfiltered variants as passing/failing. | 16 April 2015, 20:14:07 UTC |
| f84911d | Feiyu Du | 16 April 2015, 19:04:38 UTC | set lane_flag based on check of G::I::AR | 16 April 2015, 19:04:38 UTC |
| b292e96 | Feiyu Du | 16 April 2015, 18:44:12 UTC | missed a comma | 16 April 2015, 18:44:12 UTC |
| 14155f2 | Feiyu Du | 16 April 2015, 18:38:58 UTC | add once => 1 to obaserver | 16 April 2015, 18:38:58 UTC |
| 6e979a6 | Nathaniel Nutter | 16 April 2015, 15:56:11 UTC | Merge pull request #662 from nnutter/genome-env fix bug exposed in newer Bash versions | 16 April 2015, 15:56:11 UTC |
| 3aed8f5 | Michael J. Kiwala | 16 April 2015, 14:25:59 UTC | Revert accidental modification of jenkins submodule This reverts commit 2c00db10b3415d790b0c59044a3837351643ea5b. | 16 April 2015, 14:25:59 UTC |
| 678c36d | Chris Miller | 16 April 2015, 13:57:11 UTC | Merge pull request #666 from chrisamiller/master adding option to stop clustering in 1d | 16 April 2015, 13:57:11 UTC |
| 7036533 | Chris Miller | 16 April 2015, 13:55:40 UTC | removing is_optional | 16 April 2015, 13:55:40 UTC |
| 8e36493 | Chris Miller | 15 April 2015, 18:56:30 UTC | adding option to stop clustering in 1d | 16 April 2015, 13:54:38 UTC |
| 0b6401a | Nathaniel Nutter | 15 April 2015, 21:01:55 UTC | remove 'unknown' lock scope (superseded by 'site') | 15 April 2015, 21:01:55 UTC |
| edb0678 | Nathaniel Nutter | 15 April 2015, 20:57:10 UTC | remove 'tgisan' lock scope (superseded by 'host') | 15 April 2015, 20:57:10 UTC |
| 5f366ea | Nathaniel Nutter | 15 April 2015, 20:26:41 UTC | Merge pull request #660 from gatoravi/cnmops_fix check for empty segments | 15 April 2015, 20:26:41 UTC |
| 2c00db1 | Michael J. Kiwala | 15 April 2015, 20:23:08 UTC | Remove unnecessary `use Test::Exception` | 15 April 2015, 20:23:08 UTC |
| 5cd829f | Gue Su Chang | 15 April 2015, 19:41:27 UTC | Upgrade 2 in Genome::Model::Tools::Analysis::Coverage::MergeReadcounts and CoveragePlot | 15 April 2015, 19:41:27 UTC |
| 305240c | Susanna Siebert | 15 April 2015, 19:07:21 UTC | Merge branch 'master' of https://github.com/genome/genome into process_comparison | 15 April 2015, 19:07:21 UTC |
| 9bcdb12 | Susanna Siebert | 15 April 2015, 19:07:13 UTC | Include the target paths in the diff message | 15 April 2015, 19:07:13 UTC |
| d52e3b0 | Feiyu Du | 15 April 2015, 15:47:29 UTC | Merge pull request #1 from apregier/get_bam_file Get bam file | 15 April 2015, 15:47:29 UTC |
| 2d85829 | APipe Tester | 15 April 2015, 12:16:58 UTC | Updated `gmt` tab completion. | 15 April 2015, 12:16:58 UTC |
| 065f4bc | APipe Tester | 15 April 2015, 12:16:16 UTC | Updated `genome` tab completion. | 15 April 2015, 12:16:16 UTC |
| 1a7e279 | APipe Tester | 15 April 2015, 12:14:41 UTC | Updated class browser cache. | 15 April 2015, 12:14:41 UTC |
| 4c5f03c | apregier | 14 April 2015, 17:49:40 UTC | Use new get_bam_file interface For times when the content of the bam file is actually expected to be there (and we want to regenerate it if it is not there), use the new interface. | 14 April 2015, 20:56:23 UTC |
| 4a51c1d | apregier | 14 April 2015, 18:00:22 UTC | Add get_bam_file interface | 14 April 2015, 20:56:14 UTC |
| 727af1d | Feiyu Du | 14 April 2015, 20:31:21 UTC | use Genome::Sys->md5sum | 14 April 2015, 20:31:21 UTC |
| 1115ebe | Gue Su Chang | 14 April 2015, 20:20:11 UTC | Upgrade in Genome::Model::Tools::Analysis::Coverage::MergeReadcounts and CoveragePlot | 14 April 2015, 20:20:11 UTC |
| b2eca1e | Nathaniel Nutter | 14 April 2015, 20:10:23 UTC | Merge pull request #661 from nnutter/merged disable diagnostics when using compare_ok with binary files | 14 April 2015, 20:10:23 UTC |
