| 5574d46 | Jason Walker | 21 August 2015, 21:53:33 UTC | Merge pull request #955 from genome/revert-951-new_annotation_structure Revert "translated_unprocessed_pseudogene added to AnnotationStructures" | 21 August 2015, 21:53:33 UTC |
| 0172ca1 | Jason Walker | 21 August 2015, 21:53:16 UTC | Revert "translated_unprocessed_pseudogene added to AnnotationStructures" | 21 August 2015, 21:53:16 UTC |
| a38d6a9 | Jason Walker | 21 August 2015, 21:52:03 UTC | Merge pull request #951 from jasonwalker80/new_annotation_structure translated_unprocessed_pseudogene added to AnnotationStructures | 21 August 2015, 21:52:03 UTC |
| f07e342 | Eddie Belter | 21 August 2015, 21:15:59 UTC | Merge pull request #935 from ebelter/update-rm CRUD: remove unused update class | 21 August 2015, 21:15:59 UTC |
| ad7a012 | Anthony Brummett | 21 August 2015, 19:32:34 UTC | Merge pull request #952 from brummett/gatk-test Get test passing for new version of GATK | 21 August 2015, 19:32:34 UTC |
| 09838d6 | Anthony Brummett | 21 August 2015, 18:45:39 UTC | Get test passing for new version of GATK | 21 August 2015, 18:45:39 UTC |
| 577a22a | Allison Penner Regier | 21 August 2015, 18:37:03 UTC | Merge pull request #948 from apregier/handle_error_rate Handle error rate | 21 August 2015, 18:37:03 UTC |
| e787729 | apregier | 21 August 2015, 18:00:46 UTC | Add (minimal) test for alignment stats summary This test case failed before my fix to the error rate, and it now passes. (Before it showed 0.00 and now it shows NA) | 21 August 2015, 18:00:46 UTC |
| d661154 | Allison Penner Regier | 21 August 2015, 16:51:50 UTC | Merge pull request #947 from apregier/trio_process_fixes Trio process fixes | 21 August 2015, 16:51:50 UTC |
| 6c94c20 | Jason Walker | 21 August 2015, 16:33:12 UTC | Merge pull request #945 from tmooney/add_required_users_for_ensembl_annotation_structures Add required-users for annotation structure importer. | 21 August 2015, 16:33:12 UTC |
| 8464063 | Jason Walker | 21 August 2015, 16:30:51 UTC | Merge pull request #946 from tmooney/add_scarna_ensembl_biotype Add scaRNA as a non-coding RNA biotype. | 21 August 2015, 16:30:51 UTC |
| 9923d8a | Jason Walker | 21 August 2015, 16:17:31 UTC | Add translated_unprocessed_pseudogene to the list of coding_pseudogene biotype classes | 21 August 2015, 16:17:31 UTC |
| bb6c378 | Thomas B. Mooney | 20 August 2015, 22:32:49 UTC | Merge pull request #910 from tmooney/processing_profile_create_help Fix typo in method call in PP help generation | 20 August 2015, 22:32:49 UTC |
| f38595f | apregier | 20 August 2015, 21:01:29 UTC | Fix mistake | 20 August 2015, 21:01:29 UTC |
| 393f86c | Thomas B. Mooney | 20 August 2015, 20:35:03 UTC | Merge pull request #938 from tmooney/model_summary_reports_buildless Don't try to queue "Buildless" models. | 20 August 2015, 20:35:03 UTC |
| 7368c39 | apregier | 20 August 2015, 19:56:59 UTC | Add minimal test | 20 August 2015, 19:57:16 UTC |
| 6e7c1db | apregier | 20 August 2015, 19:44:20 UTC | Ignore diffs in error rate in the alignment stats report | 20 August 2015, 19:57:14 UTC |
| 099f2c4 | apregier | 20 August 2015, 19:24:38 UTC | If error rate is not defined on instrument data, use NA in report | 20 August 2015, 19:24:38 UTC |
| 42c9251 | apregier | 18 August 2015, 17:46:29 UTC | Also sort on region of interest set name | 20 August 2015, 19:00:34 UTC |
| 5df2ef8 | apregier | 18 August 2015, 17:18:31 UTC | Update blessed process Expected diffs are: -sort order of coverage_stats.tsv changed -library labels are now 1,2,3 rather than 5,6,7 and 26,27,28 | 20 August 2015, 19:00:33 UTC |
| b194b48 | apregier | 18 August 2015, 03:22:20 UTC | New interface and implementation for get_library_name_labels The previous implementation assigns a label for each library that the sample has in the database. We actually only want labels for the libraries that are relevant to a set of builds, which may be a subset of all possible libraries for a sample. This will change the number of indices and may change the blessed Trio process. | 20 August 2015, 19:00:33 UTC |
| 6a77139 | apregier | 18 August 2015, 03:19:51 UTC | Extract method to get the build | 20 August 2015, 19:00:32 UTC |
| a1a0285 | apregier | 18 August 2015, 03:18:21 UTC | Extract method to get the build | 20 August 2015, 19:00:32 UTC |
| ee5ca1a | apregier | 18 August 2015, 03:17:09 UTC | Sort by tumor sample name and roi This will help the file be produced in a consistent order that will help with diffing | 20 August 2015, 19:00:31 UTC |
| 1e33128 | apregier | 18 August 2015, 03:16:10 UTC | Sort by tumor sample name This will help the entries be in a consistent order to help with diffing | 20 August 2015, 19:00:31 UTC |
| c535e05 | apregier | 17 August 2015, 18:49:53 UTC | Include the object ids in the message | 20 August 2015, 19:00:30 UTC |
| 09b853a | Thomas Mooney | 20 August 2015, 18:33:02 UTC | Add scaRNA as a non-coding RNA biotype. Type information can be found here: <http://www.gencodegenes.org/gencode_biotypes.html> | 20 August 2015, 18:33:59 UTC |
| c7f0832 | APipe Tester | 20 August 2015, 12:18:21 UTC | Updated `genome` tab completion. | 20 August 2015, 12:18:21 UTC |
| 5cb9819 | Thomas Mooney | 19 August 2015, 22:09:59 UTC | Add required-users for annotation structure importer. | 19 August 2015, 22:09:59 UTC |
| 154be94 | Feiyu Du | 19 August 2015, 21:43:04 UTC | Merge pull request #944 from dufeiyu/merged_bam Rewrite get_merged_bam_to_revivify_per_lane_bam method to meet the need of removing superseded merged bams | 19 August 2015, 21:43:04 UTC |
| 22ea9bc | Thomas B. Mooney | 19 August 2015, 21:25:28 UTC | Merge pull request #942 from tmooney/faster_reconcile_genotype Reconcile Genotype: Make a lookup hash for the attributes. | 19 August 2015, 21:25:28 UTC |
| c5c4aaa | Feiyu Du | 19 August 2015, 20:10:31 UTC | fix speedseq.t | 19 August 2015, 20:10:31 UTC |
| ff32129 | Feiyu Du | 19 August 2015, 20:09:18 UTC | remove unnecessary else block | 19 August 2015, 20:09:18 UTC |
| 9908cf1 | Feiyu Du | 19 August 2015, 18:58:16 UTC | use get_active_merged_alignment_results instead of get_unarchived_merged_alignment_results | 19 August 2015, 18:58:16 UTC |
| c4ff441 | Thomas B. Mooney | 19 August 2015, 17:19:14 UTC | Merge pull request #943 from tmooney/add_required_users_for_ensembl_importer Add required users to Ensembl import runner. | 19 August 2015, 17:19:14 UTC |
| 1aa7114 | Thomas Mooney | 19 August 2015, 15:59:56 UTC | Add required users to Ensembl import runner. | 19 August 2015, 15:59:56 UTC |
| be37b43 | Feiyu Du | 19 August 2015, 15:46:39 UTC | test rewritten get_merged_bam_to_revivify_per_lane_bam in unit test | 19 August 2015, 15:46:39 UTC |
| e898ec3 | Avinash Ramu | 19 August 2015, 15:41:56 UTC | Merge pull request #937 from gatoravi/clinseq_resource Add lsf param to CreateMutationSpectrum | 19 August 2015, 15:41:56 UTC |
| 9066fe6 | Chris Miller | 19 August 2015, 15:10:20 UTC | Merge pull request #940 from chrisamiller/pairoscope updating default version to 0.4 to fix ensembl transcript issues | 19 August 2015, 15:10:20 UTC |
| 8aa6294 | Feiyu Du | 18 August 2015, 22:15:23 UTC | remove unnecessary bam check | 18 August 2015, 22:15:23 UTC |
| a121430 | Feiyu Du | 18 August 2015, 22:12:06 UTC | rewrite get_merged_bam_to_revivify_per_lane_bam method to get merged bam from available sources instead of smallest merged results since some superseded merged bam will be deleted | 18 August 2015, 22:12:06 UTC |
| 8a402c3 | Thomas Mooney | 18 August 2015, 20:27:25 UTC | Make a lookup hash for the attributes. This avoids searching through a list with tens of thousands of items! | 18 August 2015, 20:27:25 UTC |
| f853795 | Avinash Ramu | 18 August 2015, 18:49:44 UTC | Update resource requirement. | 18 August 2015, 18:49:44 UTC |
| e5139e1 | Chris Miller | 18 August 2015, 18:29:42 UTC | updating default version to 0.4 to fix ensembl transcript issues | 18 August 2015, 18:29:42 UTC |
| f1d99a7 | Thomas B. Mooney | 18 August 2015, 15:48:03 UTC | Merge pull request #922 from tmooney/cleanup_warnings_in_composite_workflow_test Cleanup warnings in composite workflow test. | 18 August 2015, 15:48:03 UTC |
| 848d94d | Avinash Ramu | 18 August 2015, 14:56:59 UTC | Merge pull request #936 from gatoravi/modify_mutspec Attempt to fix MutationSpectrumSequenceContext | 18 August 2015, 14:56:59 UTC |
| 2b87660 | APipe Tester | 18 August 2015, 13:34:18 UTC | updated jenkins submodule to 762fd5c | 18 August 2015, 13:34:18 UTC |
| 6e2e257 | APipe Tester | 18 August 2015, 13:34:11 UTC | updated ur submodule to 522857b | 18 August 2015, 13:34:11 UTC |
| a423c78 | APipe Tester | 18 August 2015, 12:18:19 UTC | Updated `gmt` tab completion. | 18 August 2015, 12:18:19 UTC |
| 38423c5 | APipe Tester | 18 August 2015, 12:17:30 UTC | Updated `genome` tab completion. | 18 August 2015, 12:17:30 UTC |
| bc84bed | APipe Tester | 18 August 2015, 12:15:45 UTC | Updated class browser cache. | 18 August 2015, 12:15:45 UTC |
| face6b1 | Thomas Mooney | 17 August 2015, 20:56:39 UTC | Don't try to queue "Buildless" models. | 17 August 2015, 20:56:39 UTC |
| 0cfe513 | Allison Penner Regier | 17 August 2015, 20:27:22 UTC | Merge pull request #933 from apregier/ignore_strelka_diffs Ignore strelka subdirectory | 17 August 2015, 20:27:22 UTC |
| 1a34b65 | Allison Penner Regier | 17 August 2015, 20:18:09 UTC | Merge pull request #934 from apregier/dedup_cle_test Deduplicate between config and prime-db script | 17 August 2015, 20:18:09 UTC |
| 4c4ad43 | Avinash Ramu | 17 August 2015, 19:56:43 UTC | Add lsf param | 17 August 2015, 19:56:43 UTC |
| 80ce372 | apregier | 17 August 2015, 18:57:43 UTC | Fix test | 17 August 2015, 18:57:43 UTC |
| 91569e0 | apregier | 17 August 2015, 18:38:30 UTC | Skip more specific files I was concerned that skipping any directory with 'output' in the name might lead to unintended consequences | 17 August 2015, 18:38:30 UTC |
| 1eeaf7b | Thomas B. Mooney | 17 August 2015, 18:25:38 UTC | Merge pull request #929 from tmooney/gatk_base_is_more_like_picard_base Make GATK Base more like Picard Base | 17 August 2015, 18:25:38 UTC |
| 77d4c55 | apregier | 17 August 2015, 16:39:41 UTC | Use common implementation | 17 August 2015, 16:39:41 UTC |
| 1c2138a | apregier | 17 August 2015, 16:38:14 UTC | Move use statement to top of file | 17 August 2015, 16:38:14 UTC |
| 8eb61d1 | apregier | 17 August 2015, 16:37:47 UTC | Move all object ids into config | 17 August 2015, 16:37:47 UTC |
| 650d2b3 | apregier | 17 August 2015, 16:37:04 UTC | Use more robust yaml parsing library | 17 August 2015, 16:37:04 UTC |
| a26680b | Avinash Ramu | 17 August 2015, 16:18:47 UTC | Write to temporary output file. | 17 August 2015, 16:18:47 UTC |
| b6734b7 | Jason Walker | 17 August 2015, 15:07:28 UTC | Merge pull request #917 from jasonwalker80/qc_build_metrics QC framework build metrics | 17 August 2015, 15:07:28 UTC |
| 2faa3de | Thomas Mooney | 17 August 2015, 14:36:22 UTC | Add a test for the base class. | 17 August 2015, 14:36:22 UTC |
| 82eda28 | Susanna Siebert | 17 August 2015, 14:32:13 UTC | Merge pull request #930 from susannasiebert/qc_framework_verify_bam_id_ignoreRG verifyBamId: Make the --ignoreRG param optional | 17 August 2015, 14:32:13 UTC |
| c5348d2 | Jason Walker | 17 August 2015, 14:24:40 UTC | Replace unless() with if(). | 17 August 2015, 14:24:40 UTC |
| f9a114a | Jason Walker | 17 August 2015, 14:23:08 UTC | Update whitespace. | 17 August 2015, 14:23:08 UTC |
| a376dee | Thomas B. Mooney | 17 August 2015, 13:59:41 UTC | Merge pull request #925 from tmooney/remove_unused_code_in_somval_refcov Remove unused variables and the logic to set them. | 17 August 2015, 13:59:41 UTC |
| 0ee3989 | Thomas B. Mooney | 17 August 2015, 13:59:24 UTC | Merge pull request #928 from tmooney/remove_spurious_gatk_tool_tree Remove spurious Genome/Model/Gatk.pm copy of Genome/Model/Tools/Gatk.pm | 17 August 2015, 13:59:24 UTC |
| 5dd729a | Eddie Belter | 15 August 2015, 00:25:54 UTC | CRUD: remove unused update class | 15 August 2015, 00:25:54 UTC |
| 6878b89 | apregier | 14 August 2015, 21:59:33 UTC | Need to look only for output in dir name The script is comparing absolute paths, which doesn't include any of the symlink names | 14 August 2015, 21:59:33 UTC |
| be68492 | Jason Walker | 14 August 2015, 20:22:34 UTC | Add an optional output file to build metrics. Add test to compare output file to expected. | 14 August 2015, 20:22:34 UTC |
| af3b685 | apregier | 14 August 2015, 18:42:37 UTC | Deduplicate between config and prime-db script Some of the items from config are also needed in the prime db script We might consider putting all of the items needed in the prime db script in the config, but that might also be confusing, I'm not sure | 14 August 2015, 18:46:48 UTC |
| 2a1bd02 | apregier | 14 August 2015, 16:14:57 UTC | Ignore strelka subdirectory The important strelka results will be diffed in the vcf files. The remaining files in this directory are intermediate files and contain a lot of non-diffable items like times and file paths.. | 14 August 2015, 16:14:57 UTC |
| c1dff7e | Allison Penner Regier | 14 August 2015, 16:14:12 UTC | Merge pull request #923 from apregier/cle-test Add script to prime testdb for cle test | 14 August 2015, 16:14:12 UTC |
| e50ee1c | Eddie Belter | 13 August 2015, 20:11:54 UTC | Merge pull request #927 from ebelter/volume-sync-usage Disk Volume Sync Command Updates | 13 August 2015, 20:11:54 UTC |
| 60cc3a9 | Eddie Belter | 13 August 2015, 20:11:40 UTC | Merge pull request #918 from ebelter/gc-with-perens Genotype Concordance: Allow samples with parens to run | 13 August 2015, 20:11:40 UTC |
| 70c5faf | apregier | 13 August 2015, 16:44:41 UTC | Add ensembl results for vep annotation | 13 August 2015, 16:44:41 UTC |
| aa0a182 | apregier | 13 August 2015, 16:44:05 UTC | Fix typo in feature list id | 13 August 2015, 16:44:05 UTC |
| 30afa57 | Susanna Siebert | 13 August 2015, 15:15:24 UTC | Make the --ignoreRG param optional | 13 August 2015, 15:31:00 UTC |
| bb9cbd5 | APipe Tester | 13 August 2015, 12:18:34 UTC | Updated `genome` tab completion. | 13 August 2015, 12:18:34 UTC |
| 84ebe29 | APipe Tester | 13 August 2015, 12:16:54 UTC | Updated class browser cache. | 13 August 2015, 12:16:54 UTC |
| 82810c6 | Thomas Mooney | 12 August 2015, 22:22:30 UTC | Update IndelRealigner to new GATK Base. | 12 August 2015, 22:55:37 UTC |
| 21be183 | Eddie Belter | 12 August 2015, 22:52:44 UTC | Disk Volume Sync Usage: add try/catch back | 12 August 2015, 22:52:44 UTC |
| 64585fa | Eddie Belter | 12 August 2015, 22:10:04 UTC | Disk Volume Sync Usage: add test for unmounted volume | 12 August 2015, 22:10:04 UTC |
| 952337f | Thomas Mooney | 12 August 2015, 22:05:41 UTC | Add new post-process feature to Base so don't need to override execute. | 12 August 2015, 22:05:41 UTC |
| 6e51a7a | Thomas Mooney | 12 August 2015, 21:59:29 UTC | Update RealignerTargetCreator to new GATK Base. | 12 August 2015, 21:59:29 UTC |
| afb6dd7 | Thomas Mooney | 12 August 2015, 21:53:37 UTC | Update PrintReads to use new GATK Base. | 12 August 2015, 21:53:37 UTC |
| 251c1bc | Thomas Mooney | 12 August 2015, 21:52:29 UTC | Update BaseRecalibrator to new GATK Base. | 12 August 2015, 21:52:29 UTC |
| ef853a7 | Thomas Mooney | 12 August 2015, 21:51:55 UTC | Update role classes to new GATK base. | 12 August 2015, 21:51:55 UTC |
| 0b3d811 | Thomas Mooney | 12 August 2015, 21:49:49 UTC | Add new command-line construction features to GATK Base. | 12 August 2015, 21:49:49 UTC |
| d37fda4 | Eddie Belter | 12 August 2015, 21:14:28 UTC | Disk Volume: remove sync_usage function This was only used in a test | 12 August 2015, 21:14:38 UTC |
| 29f2219 | Eddie Belter | 12 August 2015, 20:52:04 UTC | Disk Volumne Sync Usage: use subtests | 12 August 2015, 20:53:20 UTC |
| bc318ec | Thomas Mooney | 12 August 2015, 20:36:16 UTC | Update to Command::V2. | 12 August 2015, 20:36:16 UTC |
| 166fca5 | Thomas Mooney | 12 August 2015, 20:36:06 UTC | Remove unused includes. | 12 August 2015, 20:36:06 UTC |
| f1feaac | Jason Walker | 12 August 2015, 20:31:07 UTC | Add a build as an optional input to the alignment result test factory. This avoids making multiple test builds and both alignment_result and qc_result are build results. | 12 August 2015, 20:31:07 UTC |
| 9d64188 | Thomas Mooney | 12 August 2015, 20:27:45 UTC | Remove spurious Genome/Model/Gatk.pm copy of Genome/Model/Tools/Gatk.pm * Also remove Genome/Model/Gatk.t, whose testcase is covered by Genome/Model/Tools/Soap.t. | 12 August 2015, 20:27:45 UTC |
| 343d4a3 | Jason Walker | 12 August 2015, 20:27:13 UTC | Add Qc Result test factory and use in test case for command. | 12 August 2015, 20:27:13 UTC |
| 2571a4b | Jason Walker | 12 August 2015, 18:25:50 UTC | Merge pull request #919 from jasonwalker80/inactivate_config_file Inactivate AnP Config Files | 12 August 2015, 18:25:50 UTC |
