| 135b4a1 | Allison Penner Regier | 01 September 2015, 15:43:30 UTC | Merge pull request #965 from apregier/update_blessed_process Update CLE Test | 01 September 2015, 15:43:30 UTC |
| c36c338 | Jason Walker | 01 September 2015, 15:15:24 UTC | Merge pull request #974 from jasonwalker80/basic_qc_report Basic refalign QC summary. | 01 September 2015, 15:15:24 UTC |
| c92a757 | Thomas B. Mooney | 01 September 2015, 12:54:19 UTC | Merge pull request #975 from genome/revert-969-loh_write_to_tempdir Revert "ClinSeq::LOH - Write results to temp dir first." | 01 September 2015, 12:54:19 UTC |
| ef7be06 | Thomas B. Mooney | 31 August 2015, 14:54:22 UTC | Revert "ClinSeq::LOH - Write results to temp dir first." | 31 August 2015, 14:54:22 UTC |
| e14d5cb | Jason Walker | 31 August 2015, 14:08:26 UTC | Add the removal of AdspQcSummary that was missed in last commit. | 31 August 2015, 14:08:26 UTC |
| 77c629a | APipe Tester | 29 August 2015, 12:18:45 UTC | Updated `genome` tab completion. | 29 August 2015, 12:18:45 UTC |
| 2fc0bf3 | APipe Tester | 29 August 2015, 12:16:56 UTC | Updated class browser cache. | 29 August 2015, 12:16:56 UTC |
| b264274 | Avinash Ramu | 28 August 2015, 20:17:18 UTC | Merge pull request #969 from gatoravi/loh_write_to_tempdir ClinSeq::LOH - Write results to temp dir first. | 28 August 2015, 20:17:18 UTC |
| 6695579 | Jason Walker | 28 August 2015, 19:41:46 UTC | Remove the ADSP QC command and make it applicable to all projects. | 28 August 2015, 19:41:46 UTC |
| b591225 | Feiyu Du | 28 August 2015, 18:56:48 UTC | Merge pull request #972 from dufeiyu/test_fix Update GetBamReadCountsMatrix.t with the new som-var build | 28 August 2015, 18:56:48 UTC |
| eab2ce0 | Allison Penner Regier | 28 August 2015, 18:30:50 UTC | Merge pull request #967 from apregier/add_filldb_script Script to set up the fill_db environment in which you can pull in obj… | 28 August 2015, 18:30:50 UTC |
| 70a5387 | Feiyu Du | 28 August 2015, 18:03:31 UTC | update test DB | 28 August 2015, 18:03:31 UTC |
| 96aa113 | Feiyu Du | 28 August 2015, 17:59:58 UTC | update this test with new som-var build | 28 August 2015, 17:59:58 UTC |
| 694b352 | Eddie Belter | 27 August 2015, 21:21:36 UTC | Merge pull request #939 from ebelter/bam-readcount-version Handle insert_centric Option for Bam Readcount | 27 August 2015, 21:21:36 UTC |
| b641b21 | apregier | 27 August 2015, 20:29:39 UTC | Update error message | 27 August 2015, 20:29:39 UTC |
| 4042947 | Avinash Ramu | 27 August 2015, 20:13:19 UTC | Remove stray variable | 27 August 2015, 20:13:19 UTC |
| 1dfda5b | Feiyu Du | 27 August 2015, 19:55:52 UTC | Merge pull request #968 from dufeiyu/laneqc Update lane qc blessed build in DiffBlessed.pm.YAML | 27 August 2015, 19:55:52 UTC |
| 3e99270 | Avinash Ramu | 27 August 2015, 19:12:20 UTC | Write results to temp dir This PR modifies this module to write the results to a temp dir and copy results over at the end for better performance. | 27 August 2015, 19:12:20 UTC |
| a6be65e | Thomas B. Mooney | 27 August 2015, 18:18:55 UTC | Merge pull request #912 from tmooney/disabled_configs_imply_disabled_models Disabled configs imply disabled models CHANGELOG: If a configuration for an Analysis Project has been disabled, models created from that configuration will now report their status as "Disabled". | 27 August 2015, 18:18:55 UTC |
| 3d1aca8 | Feiyu Du | 27 August 2015, 18:14:23 UTC | update lane qc blessed build | 27 August 2015, 18:14:23 UTC |
| 70c406e | apregier | 27 August 2015, 17:41:12 UTC | Script to set up the fill_db environment in which you can pull in objects from the production db into a test db | 27 August 2015, 17:41:12 UTC |
| 53b566f | David Morton | 27 August 2015, 17:38:06 UTC | Merge pull request #931 from davidlmorton/ptero_optional_inputproperties Ptero runs workflows with optional inputproperties | 27 August 2015, 17:38:06 UTC |
| 0e56556 | Thomas B. Mooney | 27 August 2015, 16:11:37 UTC | Merge pull request #914 from tmooney/model_summary_wont_retry_memlimit_failures Don't auto-retry MEMLIMIT errors and orphaned allocations. | 27 August 2015, 16:11:37 UTC |
| f9897d4 | Adam Coffman | 27 August 2015, 16:05:43 UTC | Merge pull request #881 from rfugina/dont_do_extra_work Don't do extra work that we're just going to throw away | 27 August 2015, 16:05:43 UTC |
| 4b2d3db | apregier | 26 August 2015, 21:55:04 UTC | Update blessed process for CLE test | 26 August 2015, 21:55:04 UTC |
| 152b0b8 | Eddie Belter | 26 August 2015, 19:10:39 UTC | GMT Analysis Cov Bam RC Revert checking to see if bam read count version supports insertion_centric in the gmt analysis cov bam. This will get passed to the gmt bam read count and ultimately fail. This is required at this time to catch the instances of bam read count v0.4 being used in this process. This reverts commit 551627d2f81c17d56ecd77981fb09dcb30cc8c60. | 26 August 2015, 19:10:53 UTC |
| 609911c | Thomas B. Mooney | 26 August 2015, 15:51:15 UTC | Merge pull request #958 from tmooney/skip_small_indel_validation_if_no_small_indels Skip running the small indel workflow if there aren't any small indels. | 26 August 2015, 15:51:15 UTC |
| 14d17b3 | Jason Walker | 26 August 2015, 14:36:09 UTC | Merge pull request #954 from jasonwalker80/more_new_annotation_structures More annotation structure updates to biotype map. | 26 August 2015, 14:36:09 UTC |
| 197410b | Thomas Mooney | 25 August 2015, 17:19:40 UTC | Skip running the small indel workflow if there aren't any small indels. | 25 August 2015, 17:19:40 UTC |
| 7432dcd | Jason Walker | 25 August 2015, 17:11:03 UTC | alphabetical order ncrna list | 25 August 2015, 17:11:03 UTC |
| f137fd5 | Adam Coffman | 25 August 2015, 15:28:17 UTC | Merge pull request #950 from acoffman/add_new_speedseq_freeze Add path for 0.1.0 freeze of speedseq gms branch | 25 August 2015, 15:28:17 UTC |
| cb877d9 | Adam Coffman | 24 August 2015, 20:13:55 UTC | update expected output VCF with new version | 24 August 2015, 22:33:12 UTC |
| 96a25a2 | Thomas B. Mooney | 24 August 2015, 14:34:33 UTC | Merge pull request #926 from tmooney/build_output_properties Lend functionality to "is_output" build properties. | 24 August 2015, 14:34:33 UTC |
| 04a6b72 | Thomas B. Mooney | 24 August 2015, 13:29:31 UTC | Merge pull request #949 from tmooney/qc_buildmetrics_extract_subroutine Extract metrics_for_build subroutine for programmatic convenience. | 24 August 2015, 13:29:31 UTC |
| 7b58453 | Jason Walker | 21 August 2015, 21:56:13 UTC | Add translated_unprocessed_pseudogene from PR951 to this PR to avoid merge conflict. | 21 August 2015, 21:56:13 UTC |
| 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 |
| 485ef1c | Jason Walker | 21 August 2015, 21:46:18 UTC | Several new gene biotypes added to the AnnotationStructures biotype class map. | 21 August 2015, 21:46:18 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 |
| 7bda808 | Adam Coffman | 21 August 2015, 14:16:13 UTC | update tests to run latest speedseq version | 21 August 2015, 14:16:13 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 |
| ff784f7 | Adam Coffman | 20 August 2015, 21:14:04 UTC | add path for 0.1.0 freeze of speedseq gms branch | 20 August 2015, 21:14:04 UTC |
| f38595f | apregier | 20 August 2015, 21:01:29 UTC | Fix mistake | 20 August 2015, 21:01:29 UTC |
| c44d151 | Thomas Mooney | 20 August 2015, 20:49:01 UTC | Extract metrics_for_build subroutine for programmatic convenience. | 20 August 2015, 20:49:01 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 |
| 2abfb5a | Eddie Belter | 17 August 2015, 23:00:37 UTC | GMT Analysis Cov BRC: it is called deafult_value! | 17 August 2015, 23:00:37 UTC |
| 551627d | Eddie Belter | 17 August 2015, 21:08:31 UTC | GMT Analysis Cov Bam RC: only use insert_centric if bam readcount version supports it | 17 August 2015, 21:08:31 UTC |
| 7a2a53d | Eddie Belter | 17 August 2015, 21:07:57 UTC | GMT Analysis Cov Bam RC: get default bamreadcount version from command | 17 August 2015, 21:07:57 UTC |
| 10f259d | Eddie Belter | 17 August 2015, 20:58:10 UTC | Bam Readcount: insert_centric add version_has_insertion_centric add assert_version_has_insertion_centric use assert_version_has_insertion_centric in command builder add tests | 17 August 2015, 20:58:10 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 |
| 3c2c7b5 | Eddie Belter | 17 August 2015, 20:42:48 UTC | Bam Readcount: use version built in to compare versions | 17 August 2015, 20:42:48 UTC |
| 190444e | Eddie Belter | 17 August 2015, 20:40:52 UTC | Bam Readcount: add version specific options test | 17 August 2015, 20:40:52 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 |
