| 36ceaeb | APipe Tester | 15 November 2013, 13:17:50 UTC | Updated `gmt` tab completion. | 15 November 2013, 13:17:50 UTC |
| 67cdc34 | APipe Tester | 15 November 2013, 13:17:08 UTC | Updated `genome` tab completion. | 15 November 2013, 13:17:08 UTC |
| b92eaee | APipe Tester | 15 November 2013, 13:15:27 UTC | Updated class browser cache. | 15 November 2013, 13:15:27 UTC |
| 1c2f32a | Avinash Ramu | 15 November 2013, 03:24:22 UTC | use build variable | 15 November 2013, 03:24:22 UTC |
| 84da588 | Avinash Ramu | 15 November 2013, 03:05:37 UTC | update clinseq to intersect RNA fusions with DNA SV's only if WGS build is specified | 15 November 2013, 03:18:11 UTC |
| 087e8b4 | Thomas Mooney | 14 November 2013, 23:27:16 UTC | Another check for the build to exist before asking for its data directory. | 14 November 2013, 23:27:16 UTC |
| 5a2f8b5 | Thomas Mooney | 14 November 2013, 23:24:02 UTC | Ensure we have a WGS build before asking for its data directory. | 14 November 2013, 23:24:43 UTC |
| fccd76c | Thomas Mooney | 14 November 2013, 23:23:28 UTC | More variable use instead of repeated accessor calls | 14 November 2013, 23:24:42 UTC |
| 8ff1528 | Thomas Mooney | 14 November 2013, 23:20:11 UTC | Use the variables we made instead of reasking the build every time. | 14 November 2013, 23:24:41 UTC |
| 1b0d549 | apregier | 14 November 2013, 23:22:06 UTC | Merge branch 'fireteam2' into gb_master | 14 November 2013, 23:22:06 UTC |
| 24998b5 | apregier | 14 November 2013, 22:21:31 UTC | Add a log directory for the workflow | 14 November 2013, 22:48:50 UTC |
| d02eaf8 | apregier | 14 November 2013, 21:33:37 UTC | Preload substructures for speed | 14 November 2013, 22:48:49 UTC |
| 53401d1 | apregier | 14 November 2013, 21:32:36 UTC | Run workflow with workflow object rather than xml | 14 November 2013, 22:48:48 UTC |
| 14015c7 | apregier | 13 November 2013, 20:10:28 UTC | Simplify annotate-chromosome workflow | 14 November 2013, 22:48:48 UTC |
| 692bc44 | apregier | 12 November 2013, 19:33:15 UTC | Fix bug in file format | 14 November 2013, 22:48:47 UTC |
| 9b9f649 | apregier | 10 November 2013, 21:16:15 UTC | Add "translated_processed_pseudogene" to biotype hash | 14 November 2013, 22:48:46 UTC |
| 0b5cba8 | apregier | 08 November 2013, 17:54:19 UTC | Need to create sub-directories | 14 November 2013, 22:48:46 UTC |
| 52fd443 | apregier | 08 November 2013, 17:39:56 UTC | AnnotationStructures object was not moved to Command dir | 14 November 2013, 22:48:45 UTC |
| 2d9196d | apregier | 08 November 2013, 17:31:49 UTC | Db commands were moved into Command dir | 14 November 2013, 22:48:44 UTC |
| db65891 | Jim Weible | 14 November 2013, 20:03:13 UTC | move method from old AQID | 14 November 2013, 20:03:13 UTC |
| 46ae3d5 | Eddie Belter | 14 November 2013, 18:27:00 UTC | InstData Import: add lane with value of 1 to fastq inst data when importing | 14 November 2013, 18:27:00 UTC |
| e4af768 | apregier | 14 November 2013, 17:19:01 UTC | Merge branch 'copy' into gb_master | 14 November 2013, 17:19:01 UTC |
| c56d3db | apregier | 13 November 2013, 22:50:13 UTC | Create archive tarball when requested | 14 November 2013, 16:55:12 UTC |
| 8fd983a | apregier | 12 November 2013, 22:33:27 UTC | Get the tcga-compliant files | 14 November 2013, 16:55:11 UTC |
| 0bf84eb | apregier | 12 November 2013, 16:16:24 UTC | Revise vcf file naming | 14 November 2013, 16:55:11 UTC |
| ffe5735 | apregier | 08 November 2013, 20:44:21 UTC | Add some tests | 14 November 2013, 16:55:10 UTC |
| 0b322bf | apregier | 07 November 2013, 21:14:31 UTC | Use archive name as mage-tab file names | 14 November 2013, 16:55:10 UTC |
| 6207fe9 | apregier | 06 November 2013, 21:53:37 UTC | Add option to load cghub id by tcga-name rather than just bam file | 14 November 2013, 16:55:09 UTC |
| b8441a6 | apregier | 06 November 2013, 19:29:38 UTC | Use somatic variation vcfs rather than refalign | 14 November 2013, 16:55:08 UTC |
| a81b20e | apregier | 06 November 2013, 15:39:11 UTC | Look up CGHub based on bam file | 14 November 2013, 16:55:08 UTC |
| ae1bce8 | apregier | 05 November 2013, 21:28:34 UTC | Take SomVar models as inputs | 14 November 2013, 16:55:07 UTC |
| f6d2260 | apregier | 05 November 2013, 20:46:57 UTC | Pass in cghub ids for builds | 14 November 2013, 16:55:06 UTC |
| ce626aa | apregier | 04 November 2013, 22:34:30 UTC | Hard-code capture reagent info | 14 November 2013, 16:55:06 UTC |
| 850a8d4 | apregier | 29 October 2013, 21:40:35 UTC | Add some more required sdrf columns | 14 November 2013, 16:55:05 UTC |
| c0df558 | apregier | 28 October 2013, 16:26:45 UTC | Add a couple hard-coded values | 14 November 2013, 16:55:04 UTC |
| 3bc3d98 | apregier | 25 October 2013, 21:49:44 UTC | Add some more columns to the vcf row | 14 November 2013, 16:55:04 UTC |
| 555c591 | apregier | 25 October 2013, 21:06:35 UTC | Use a string object so we can preserve quoting | 14 November 2013, 16:55:02 UTC |
| daaefab | apregier | 25 October 2013, 20:05:22 UTC | Cleanup from travis | 14 November 2013, 16:55:01 UTC |
| 2efe6c9 | apregier | 25 October 2013, 20:02:54 UTC | Use undef instead of fancy string | 14 November 2013, 16:55:00 UTC |
| a8e4aff | apregier | 25 October 2013, 19:58:30 UTC | Add sample barcode and uuid to row | 14 November 2013, 16:55:00 UTC |
| 2b82e70 | apregier | 25 October 2013, 18:55:15 UTC | Vcf Header parses arbitrary metainfo lines | 14 November 2013, 16:54:59 UTC |
| 0a7f40b | apregier | 25 October 2013, 18:43:42 UTC | Allow almost everything in regular strings | 14 November 2013, 16:54:58 UTC |
| 53321ca | apregier | 25 October 2013, 18:28:11 UTC | Allow arbitrary strings | 14 November 2013, 16:54:58 UTC |
| e2584cf | apregier | 25 October 2013, 17:40:24 UTC | Fix bug with perl_quotelike | 14 November 2013, 16:54:57 UTC |
| a292846 | apregier | 25 October 2013, 16:35:26 UTC | Store flags specially | 14 November 2013, 16:54:57 UTC |
| 32a7c37 | apregier | 24 October 2013, 21:05:06 UTC | Parser for metainformation lines in vcf headers | 14 November 2013, 16:54:56 UTC |
| a798e31 | apregier | 23 October 2013, 20:29:40 UTC | Implement intial methods for create-submission-archive | 14 November 2013, 16:54:55 UTC |
| 60de48c | Thomas Mooney | 14 November 2013, 14:46:55 UTC | New point release of joinx changes the output. | 14 November 2013, 14:46:55 UTC |
| 8aafd93 | APipe Tester | 14 November 2013, 13:16:25 UTC | Updated `genome` tab completion. | 14 November 2013, 13:16:25 UTC |
| f18a020 | dmorton | 14 November 2013, 01:25:09 UTC | Fix inadvertant submodule revision change | 14 November 2013, 01:25:09 UTC |
| 49b9f9e | dmorton | 14 November 2013, 01:12:04 UTC | Can specify lsf_queue lsf_resource and lsf_project to Commands | 14 November 2013, 01:12:04 UTC |
| b23a0c2 | dmorton | 14 November 2013, 01:02:52 UTC | Add test for operation_type_attributes | 14 November 2013, 01:03:35 UTC |
| 31aaa65 | Adam Coffman | 13 November 2013, 23:49:39 UTC | support re-processing of failed inst data in CQID | 13 November 2013, 23:49:39 UTC |
| ad498f0 | Thomas Mooney | 13 November 2013, 21:14:49 UTC | Allow UR to efficiently load the entities instead of doing N+1 queries. | 13 November 2013, 21:14:49 UTC |
| 216bc2a | Ian Ferguson | 11 November 2013, 19:01:03 UTC | Skip BamQc error_rate on bwamem 0.7.5a | 13 November 2013, 19:44:47 UTC |
| 34ca6ce | Ian Ferguson | 08 November 2013, 21:41:54 UTC | Fix CPU count (-t) parameter handling in Bwamem | 13 November 2013, 19:44:47 UTC |
| 32df466 | Ian Ferguson | 08 November 2013, 21:39:21 UTC | Fix _check_read_count in Bwamem for 0x800 flag | 13 November 2013, 19:44:46 UTC |
| e3d26dc | Ian Ferguson | 25 October 2013, 19:31:33 UTC | Parameter handling in AlignmentResult/Bwamem. | 13 November 2013, 19:44:45 UTC |
| 65b411e | Ian Ferguson | 25 October 2013, 19:18:39 UTC | Use debug_message in AlignmentResult/Bwamem. | 13 November 2013, 19:44:45 UTC |
| 7e3cae8 | Ian Ferguson | 25 October 2013, 19:11:15 UTC | Add 'supplementary_alignment_flag' to GMT::Bwa Add 'supplementary_alignment_flag' feature to GMT::Bwa. This feature is available (so far) in Bwa 0.7.5 and 0.7.5a. | 13 November 2013, 19:44:44 UTC |
| 529ec1d | APipe Tester | 13 November 2013, 17:32:48 UTC | updated graphite submodule to 633dbaf | 13 November 2013, 17:32:48 UTC |
| 0dff8b7 | APipe Tester | 13 November 2013, 16:53:42 UTC | updated workflow submodule to 3e6e44d | 13 November 2013, 16:53:42 UTC |
| 45cf87a | APipe Tester | 13 November 2013, 16:44:35 UTC | updated jenkins submodule to b02fcf4 | 13 November 2013, 16:44:35 UTC |
| c3c0cdd | APipe Tester | 13 November 2013, 16:40:55 UTC | updated graphite submodule to fc842eb | 13 November 2013, 16:40:55 UTC |
| d148284 | APipe Tester | 13 November 2013, 16:40:49 UTC | updated ur submodule to 92e82aa | 13 November 2013, 16:40:49 UTC |
| fa30572 | Thomas Mooney | 13 November 2013, 15:56:26 UTC | Only request a new build if we need one. | 13 November 2013, 15:56:26 UTC |
| 2746854 | Thomas Mooney | 13 November 2013, 14:18:33 UTC | Spelling: chromsome => chromosome | 13 November 2013, 14:18:33 UTC |
| b14529b | Thomas Mooney | 13 November 2013, 14:15:32 UTC | Spelling: chromsomes => chromosomes | 13 November 2013, 14:15:32 UTC |
| d8926e7 | Adam Coffman | 12 November 2013, 22:16:41 UTC | only sync bridge elements when we have already synced the inst data | 12 November 2013, 22:16:41 UTC |
| cd65d4a | Anthony Brummett | 12 November 2013, 20:49:12 UTC | Remove IP address for the test database | 12 November 2013, 21:50:44 UTC |
| 5706969 | Anthony Brummett | 12 November 2013, 20:45:11 UTC | index on config.instrument_data_analysis_project_bridge.analysis_project_id | 12 November 2013, 21:50:43 UTC |
| a0ec573 | Anthony Brummett | 12 November 2013, 20:42:48 UTC | index on config.instrument_data_analysis_project_bridge.instrument_data_id | 12 November 2013, 21:50:43 UTC |
| 7f11693 | Anthony Brummett | 12 November 2013, 20:40:21 UTC | index on config.instrument_data_analysis_project_bridge.fail_count | 12 November 2013, 21:50:42 UTC |
| 676fad3 | Anthony Brummett | 12 November 2013, 20:37:51 UTC | index on config.instrument_data_analysis_project_bridge.status | 12 November 2013, 21:50:42 UTC |
| 0e95511 | Anthony Brummett | 12 November 2013, 20:29:07 UTC | add table config.instrument_data_analysis_project_bridge | 12 November 2013, 21:50:41 UTC |
| 0eea766 | Anthony Brummett | 07 November 2013, 17:19:17 UTC | permission on web.task_params | 12 November 2013, 21:50:40 UTC |
| 2cdf3b0 | Anthony Brummett | 07 November 2013, 17:19:12 UTC | permission on web.task | 12 November 2013, 21:50:40 UTC |
| f0abb57 | Anthony Brummett | 07 November 2013, 17:19:09 UTC | permission on web.search_index_queue | 12 November 2013, 21:50:39 UTC |
| 01bc33f | Anthony Brummett | 07 November 2013, 17:19:03 UTC | permission on web.nomenclature_field | 12 November 2013, 21:50:39 UTC |
| 1745150 | Anthony Brummett | 07 November 2013, 17:18:59 UTC | permission on web.nomenclature_enum_value | 12 November 2013, 21:50:38 UTC |
| adbd79f | Anthony Brummett | 07 November 2013, 17:18:51 UTC | permission on web.nomenclature | 12 November 2013, 21:50:38 UTC |
| 71dd605 | Anthony Brummett | 05 November 2013, 17:15:27 UTC | index on web.search_index_queue.priority | 12 November 2013, 21:50:37 UTC |
| 80cacb7 | Anthony Brummett | 05 November 2013, 17:15:08 UTC | index on web.nomenclature.name | 12 November 2013, 21:50:36 UTC |
| 3367329 | Anthony Brummett | 05 November 2013, 17:14:57 UTC | index on web.nomenclature_field.nomenclature_id | 12 November 2013, 21:50:36 UTC |
| e4447e1 | Anthony Brummett | 05 November 2013, 17:14:48 UTC | index on web.nomenclature_enum_value.nomenclature_field_id | 12 November 2013, 21:50:35 UTC |
| 5a93760 | Anthony Brummett | 31 October 2013, 17:27:56 UTC | add table web.task_params | 12 November 2013, 21:50:35 UTC |
| 5c7e392 | Anthony Brummett | 31 October 2013, 17:26:20 UTC | add table web.task | 12 November 2013, 21:50:34 UTC |
| 9e20834 | Anthony Brummett | 31 October 2013, 17:23:47 UTC | add table web.search_index_queue | 12 November 2013, 21:50:34 UTC |
| 1428a91 | Anthony Brummett | 31 October 2013, 17:19:59 UTC | add table web.nomenclature_enum_value | 12 November 2013, 21:50:33 UTC |
| 3cee9e5 | Anthony Brummett | 31 October 2013, 17:17:29 UTC | add table web.nomenclature_field | 12 November 2013, 21:50:32 UTC |
| ef7b891 | Anthony Brummett | 31 October 2013, 17:17:06 UTC | add table web.nomenclature | 12 November 2013, 21:50:32 UTC |
| 65f67b6 | Anthony Brummett | 06 November 2013, 21:58:26 UTC | permission on web schema | 12 November 2013, 21:50:31 UTC |
| a3b8dd8 | Anthony Brummett | 31 October 2013, 17:10:02 UTC | add web schema | 12 November 2013, 21:50:31 UTC |
| 6a292f4 | Anthony Brummett | 07 November 2013, 17:17:41 UTC | permission on subject.pairing | 12 November 2013, 21:50:30 UTC |
| 2e2e9d6 | Anthony Brummett | 31 October 2013, 16:16:42 UTC | add table subject.pairing | 12 November 2013, 21:50:29 UTC |
| 79de794 | Anthony Brummett | 07 November 2013, 17:00:54 UTC | permission on config.set | 12 November 2013, 21:50:29 UTC |
| f0c2b28 | Anthony Brummett | 07 November 2013, 17:00:32 UTC | permission on config.analysis_project | 12 November 2013, 21:50:28 UTC |
| 73e92ae | Anthony Brummett | 07 November 2013, 16:58:07 UTC | permission on config.analysis_menu_item | 12 November 2013, 21:50:28 UTC |
| ef20c59 | Anthony Brummett | 04 November 2013, 21:08:43 UTC | index in config.set.allocation_id | 12 November 2013, 21:50:27 UTC |
| 0e8550e | Anthony Brummett | 01 November 2013, 19:19:40 UTC | index on config.analysis_project.configuration_set_id | 12 November 2013, 21:50:27 UTC |
