| 518a504 | Anthony Brummett | 17 April 2014, 19:20:10 UTC | extract method to get the insert size metrics | 17 April 2014, 20:46:27 UTC |
| 748fb81 | Anthony Brummett | 17 April 2014, 16:36:04 UTC | extract method to get the error rate metrics | 17 April 2014, 20:46:27 UTC |
| 096de4d | Anthony Brummett | 17 April 2014, 16:32:23 UTC | make a class to represent a label+directory pair | 17 April 2014, 20:46:26 UTC |
| 61a9eeb | Anthony Brummett | 17 April 2014, 16:00:27 UTC | extract method to get the mark duplicates metrics | 17 April 2014, 20:46:25 UTC |
| cc0fb12 | Anthony Brummett | 17 April 2014, 15:51:50 UTC | extract method to get the alignment summary metric data from an output dir | 17 April 2014, 20:46:25 UTC |
| f48f393 | Anthony Brummett | 17 April 2014, 15:37:03 UTC | extract methods to turn the text list of things into Perl lists | 17 April 2014, 20:46:24 UTC |
| 36d7a31 | Anthony Brummett | 17 April 2014, 15:33:24 UTC | extract method to create writer | 17 April 2014, 20:46:24 UTC |
| e505fc5 | Anthony Brummett | 17 April 2014, 15:32:19 UTC | extract method to validate labels and directories have the same number of members | 17 April 2014, 20:46:23 UTC |
| 4d9b7a2 | Anthony Brummett | 17 April 2014, 15:14:58 UTC | remove breakpoint | 17 April 2014, 20:46:23 UTC |
| 385985a | Anthony Brummett | 17 April 2014, 15:13:08 UTC | remove unnecessary variable | 17 April 2014, 20:46:22 UTC |
| 7174f63 | Anthony Brummett | 16 April 2014, 19:15:39 UTC | Get in_place_of_null_value set to enpty-string unless otherwise specified The UR mutator wasn't seeing that undef was different than empty string, which matches UR behavior in other places | 17 April 2014, 20:46:21 UTC |
| b7c9653 | Anthony Brummett | 16 April 2014, 19:13:20 UTC | avoid an uninitialized value warning by checking for undef the right way | 17 April 2014, 20:46:21 UTC |
| 300f9a4 | Anthony Brummett | 16 April 2014, 19:12:46 UTC | The ErrorRate files can have comments at the top of them | 17 April 2014, 20:46:20 UTC |
| 2168773 | APipe Tester | 17 April 2014, 20:44:20 UTC | updated workflow submodule to e975bcf | 17 April 2014, 20:44:20 UTC |
| 78e02e5 | Feiyu Du | 17 April 2014, 20:24:33 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 17 April 2014, 20:24:33 UTC |
| f300b31 | Feiyu Du | 17 April 2014, 20:24:27 UTC | add lsf_resource to copycat somatic | 17 April 2014, 20:24:27 UTC |
| caac238 | Nathaniel Nutter | 17 April 2014, 20:19:28 UTC | update UR submodule URL | 17 April 2014, 20:19:28 UTC |
| 5a27199 | Adam Coffman | 17 April 2014, 15:50:59 UTC | update brc46 regex on sample importer to support CSB | 17 April 2014, 15:50:59 UTC |
| 3a23021 | dmorton | 17 April 2014, 15:18:31 UTC | Pull output_file_path into base class | 17 April 2014, 15:28:25 UTC |
| 9ee42e6 | dmorton | 17 April 2014, 15:16:00 UTC | whitespace | 17 April 2014, 15:28:25 UTC |
| 7ffcbd1 | dmorton | 17 April 2014, 15:15:12 UTC | All Annotation::Detail::Commands and Results have input_result input | 17 April 2014, 15:28:25 UTC |
| acf833a | dmorton | 17 April 2014, 14:57:13 UTC | Add output_file_path as interface in base Result class | 17 April 2014, 14:57:13 UTC |
| 3bc3237 | dmorton | 17 April 2014, 13:51:04 UTC | whitespace | 17 April 2014, 13:51:04 UTC |
| 055092b | dmorton | 16 April 2014, 21:54:58 UTC | Rename AddReadcounts to Readcount | 17 April 2014, 13:49:52 UTC |
| 9982f12 | dmorton | 16 April 2014, 21:42:49 UTC | Renamed Readcount to RunBamReadcount | 17 April 2014, 13:49:52 UTC |
| a9eefb1 | dmorton | 16 April 2014, 21:35:34 UTC | Renamed JoinxVcfAnnotate to just Joinx It is already in the Annotation directory. | 17 April 2014, 13:49:51 UTC |
| 6433e7c | APipe Tester | 17 April 2014, 12:17:54 UTC | Updated `genome` tab completion. | 17 April 2014, 12:17:54 UTC |
| a44d496 | APipe Tester | 17 April 2014, 12:16:25 UTC | Updated class browser cache. | 17 April 2014, 12:16:25 UTC |
| 23ca9a2 | Avinash Ramu | 17 April 2014, 03:56:14 UTC | remove whitespace at end of line | 17 April 2014, 03:56:14 UTC |
| 098809a | Avinash Ramu | 17 April 2014, 00:28:18 UTC | update clinseq blessed build | 17 April 2014, 00:29:02 UTC |
| 583ce8e | Avinash Ramu | 16 April 2014, 23:04:00 UTC | update test build for makecircosplot | 17 April 2014, 00:29:01 UTC |
| 07a3f89 | Avinash Ramu | 16 April 2014, 23:03:12 UTC | look in samtools results for snv sources | 17 April 2014, 00:28:59 UTC |
| 9acf9eb | Avinash Ramu | 16 April 2014, 21:07:18 UTC | update test-data directory | 17 April 2014, 00:28:59 UTC |
| 9bf5506 | Avinash Ramu | 16 April 2014, 20:59:25 UTC | change expected number of diffs | 17 April 2014, 00:28:58 UTC |
| 259b49d | Avinash Ramu | 16 April 2014, 19:01:15 UTC | update test directory | 17 April 2014, 00:28:57 UTC |
| 2a5b88b | Avinash Ramu | 16 April 2014, 19:00:50 UTC | remove output of build_dir | 17 April 2014, 00:28:56 UTC |
| e345665 | Avinash Ramu | 16 April 2014, 15:29:00 UTC | update location of fusion file within clinseq build | 17 April 2014, 00:28:55 UTC |
| 34f32f0 | Avinash Ramu | 16 April 2014, 15:28:31 UTC | don't die if BAMQC results already. | 17 April 2014, 00:28:55 UTC |
| f7002ee | Avinash Ramu | 16 April 2014, 15:27:23 UTC | use a hash reference directly | 17 April 2014, 00:28:54 UTC |
| ed246b5 | Avinash Ramu | 16 April 2014, 15:24:53 UTC | refactor get_common_name | 17 April 2014, 00:28:53 UTC |
| 94e6dfa | Avinash Ramu | 16 April 2014, 15:24:22 UTC | get perlane bamqc and per build bamqc reports | 17 April 2014, 00:28:53 UTC |
| ebf487b | Avinash Ramu | 15 April 2014, 15:22:22 UTC | add test for InstrumentDataAlignmentBams | 17 April 2014, 00:28:52 UTC |
| bc55023 | Avinash Ramu | 15 April 2014, 15:18:36 UTC | add method to access lane/bamqcpath easily | 17 April 2014, 00:28:51 UTC |
| 5fe7d35 | Avinash Ramu | 14 April 2014, 20:06:47 UTC | reorganize fusion files' location | 17 April 2014, 00:28:51 UTC |
| 78bed09 | Avinash Ramu | 14 April 2014, 19:55:30 UTC | refactor summarize_builds 1 | 17 April 2014, 00:28:50 UTC |
| c5d9156 | Avinash Ramu | 14 April 2014, 19:54:20 UTC | use tsv reader instead of awk to parse files | 17 April 2014, 00:28:50 UTC |
| 3aa58f7 | apregier | 16 April 2014, 22:09:20 UTC | Merge branch 'updated' into gb_master | 16 April 2014, 22:09:20 UTC |
| f43268f | apregier | 16 April 2014, 22:02:09 UTC | annotation_builds input is many Multiple builds aren't currently supported but this way we can implement it without changing the software result input | 16 April 2014, 22:02:09 UTC |
| 75d611f | apregier | 16 April 2014, 21:50:08 UTC | Imported variation list build is input on result | 16 April 2014, 21:50:08 UTC |
| e05586e | apregier | 16 April 2014, 21:20:48 UTC | Merge branch 'updated' into gb_master | 16 April 2014, 21:20:48 UTC |
| 80e4f93 | apregier | 16 April 2014, 21:11:33 UTC | Use more complete set of params for vep | 16 April 2014, 21:13:49 UTC |
| 022c998 | apregier | 16 April 2014, 21:09:58 UTC | Use generic list of feature lists rather than enumerating them | 16 April 2014, 21:13:48 UTC |
| b912ba2 | apregier | 16 April 2014, 21:07:25 UTC | Use vep run instead of vep | 16 April 2014, 21:13:48 UTC |
| 1e8f2cf | apregier | 16 April 2014, 21:01:24 UTC | Make db ensembl run command tree | 16 April 2014, 21:13:47 UTC |
| 5e3db1d | Tiandao Li | 16 April 2014, 20:52:49 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 April 2014, 20:52:49 UTC |
| 224774a | Tiandao Li | 16 April 2014, 20:52:10 UTC | temp folder and less than 1 min | 16 April 2014, 20:52:10 UTC |
| eb951e2 | Adam Coffman | 16 April 2014, 20:12:42 UTC | Bump vcf_version due to joinx update | 16 April 2014, 20:12:42 UTC |
| fcba147 | Tiandao Li | 16 April 2014, 19:41:56 UTC | changes | 16 April 2014, 19:41:56 UTC |
| 8e5d77b | Ben Ainscough | 16 April 2014, 18:13:04 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 April 2014, 18:13:04 UTC |
| cea6536 | Ben Ainscough | 16 April 2014, 18:11:31 UTC | added more robust reference sequence build check | 16 April 2014, 18:11:31 UTC |
| fe8859a | dmorton | 16 April 2014, 15:52:20 UTC | Remove WithSoftwareResult | 16 April 2014, 16:04:49 UTC |
| ed410d4 | Ian Ferguson | 16 April 2014, 16:01:20 UTC | Remove unused GMTCuffdiffWrapper | 16 April 2014, 16:01:20 UTC |
| 44f740a | Thomas Mooney | 16 April 2014, 13:21:17 UTC | Update the username on all events when using run_as. That way commands like `genome model build abandon` don't complain about events owned by other users. | 16 April 2014, 13:21:17 UTC |
| 61b8b89 | apregier | 15 April 2014, 22:00:14 UTC | Merge branch 'updated' into gb_master | 15 April 2014, 22:00:14 UTC |
| cdefba1 | apregier | 15 April 2014, 21:55:37 UTC | Add a new interface to vep command Gets the api and cache through the ensembl version instead of the annotation build | 15 April 2014, 21:58:34 UTC |
| a0fe4a2 | apregier | 15 April 2014, 21:28:56 UTC | Put most functionality into a base class | 15 April 2014, 21:58:32 UTC |
| 5f28ead | apregier | 15 April 2014, 20:15:59 UTC | Move stage method to cache object | 15 April 2014, 21:58:30 UTC |
| e07ab68 | apregier | 15 April 2014, 20:02:49 UTC | whitespace | 15 April 2014, 21:58:29 UTC |
| 6b8a858 | apregier | 15 April 2014, 20:01:46 UTC | Use plugin object | 15 April 2014, 21:58:28 UTC |
| 2191537 | apregier | 15 April 2014, 20:00:20 UTC | Make transient properties Text instead of String This way they don't get slurped in as string properties | 15 April 2014, 21:58:28 UTC |
| 34593fb | apregier | 15 April 2014, 19:59:37 UTC | Add vep plugin object | 15 April 2014, 21:58:27 UTC |
| 83654b1 | apregier | 15 April 2014, 18:21:32 UTC | Separate staging plugin config from querying for plugin args | 15 April 2014, 21:58:25 UTC |
| 84b411e | apregier | 15 April 2014, 17:23:51 UTC | Create one plugin arg string at a time | 15 April 2014, 21:58:24 UTC |
| 1a8d4b3 | apregier | 15 April 2014, 17:06:20 UTC | Extract method to get or create the temp dir | 15 April 2014, 21:58:23 UTC |
| 29ffa4e | apregier | 15 April 2014, 15:39:00 UTC | Extract methods to construct and run the command | 15 April 2014, 21:58:23 UTC |
| 3f6f5ed | apregier | 15 April 2014, 15:29:31 UTC | Extract method for db_connect params | 15 April 2014, 21:58:22 UTC |
| 2931e87 | apregier | 15 April 2014, 15:25:04 UTC | Extract methods for plugin_args and cache_args | 15 April 2014, 21:58:21 UTC |
| 7227ceb | apregier | 15 April 2014, 14:56:27 UTC | Extract custom_args method | 15 April 2014, 21:58:21 UTC |
| 01d4112 | apregier | 15 April 2014, 14:52:41 UTC | Make accessor functions rather than local variables | 15 April 2014, 21:58:20 UTC |
| f60c49c | apregier | 15 April 2014, 14:50:17 UTC | Move string args tweaking into subroutine | 15 April 2014, 21:58:19 UTC |
| ff9b930 | APipe Tester | 15 April 2014, 20:46:24 UTC | updated jenkins submodule to c81b2ba | 15 April 2014, 20:46:24 UTC |
| c379d02 | APipe Tester | 15 April 2014, 20:34:26 UTC | updated jenkins submodule to 8363e5f | 15 April 2014, 20:34:26 UTC |
| e26c217 | Thomas Mooney | 15 April 2014, 20:19:13 UTC | Do all the sorting and filtering logic even if from an Analysis Project This change is pursuant to RT#98634. | 15 April 2014, 20:19:13 UTC |
| c69f825 | APipe Tester | 15 April 2014, 20:04:30 UTC | updated jenkins submodule to b9e8e79 | 15 April 2014, 20:04:30 UTC |
| 6ffd932 | APipe Tester | 15 April 2014, 19:55:31 UTC | updated jenkins submodule to 8c8edaa | 15 April 2014, 19:55:31 UTC |
| b2f914b | APipe Tester | 15 April 2014, 19:52:34 UTC | updated jenkins submodule to ffac64e | 15 April 2014, 19:52:34 UTC |
| 16f6353 | APipe Tester | 15 April 2014, 19:46:53 UTC | updated jenkins submodule to ad170e0 | 15 April 2014, 19:46:53 UTC |
| 3f27b04 | Thomas Mooney | 15 April 2014, 14:20:33 UTC | Update test to have less trailing whitespace. | 15 April 2014, 14:20:33 UTC |
| 081bd70 | Thomas Mooney | 15 April 2014, 14:08:51 UTC | Remove trailing whitespace. | 15 April 2014, 14:08:51 UTC |
| ee2b3ac | apregier | 15 April 2014, 14:08:16 UTC | Merge branch 'updated' into gb_master | 15 April 2014, 14:08:16 UTC |
| a6bea93 | apregier | 14 April 2014, 22:45:03 UTC | Extract method to resolve format and input file | 15 April 2014, 14:05:27 UTC |
| 48d4f56 | apregier | 14 April 2014, 22:07:51 UTC | Extract script_path method | 15 April 2014, 14:05:27 UTC |
| cbc8974 | apregier | 14 April 2014, 22:05:26 UTC | Extract annotation_build method | 15 April 2014, 14:05:25 UTC |
| 9ba5b60 | APipe Tester | 15 April 2014, 12:18:59 UTC | Updated `gmt` tab completion. | 15 April 2014, 12:18:59 UTC |
| 0c5afc2 | APipe Tester | 15 April 2014, 12:18:14 UTC | Updated `genome` tab completion. | 15 April 2014, 12:18:14 UTC |
| 0caaa3b | APipe Tester | 15 April 2014, 12:16:34 UTC | Updated class browser cache. | 15 April 2014, 12:16:34 UTC |
| d0ec257 | Gabriel Sanderson | 15 April 2014, 00:20:18 UTC | minor param cleanup | 15 April 2014, 00:20:18 UTC |
| a29e56a | Gabriel Sanderson | 15 April 2014, 00:14:57 UTC | Refactored code out of adaptor tests into an adaptor testhelper -- still could use a little cleanup with lots of parameters passing around | 15 April 2014, 00:14:57 UTC |
| 0981ab9 | Gabriel Sanderson | 14 April 2014, 22:22:22 UTC | Added SomaticValidation adaptor and test | 14 April 2014, 22:22:22 UTC |
| a16c4e2 | Gabriel Sanderson | 14 April 2014, 21:54:19 UTC | Move resolve_annotation_build up to the base class | 14 April 2014, 21:54:19 UTC |
