| 6a94784 | Thomas Mooney | 27 August 2014, 20:53:30 UTC | HACK: change the tmpdir if --keep-tmp is set. We were coincidentally deleting the /tmp before (which we wanted). Now that we sometimes need to keep it, change directories to preserve it only when we want it. Otherwise let it get removed. | 27 August 2014, 20:53:30 UTC |
| 885f1ad | APipe Tester | 27 August 2014, 18:32:30 UTC | updated graphite submodule to 09c7ddb | 27 August 2014, 18:32:30 UTC |
| eb2cb9b | APipe Tester | 27 August 2014, 18:32:23 UTC | updated jenkins submodule to 6d13341 | 27 August 2014, 18:32:23 UTC |
| c310841 | APipe Tester | 27 August 2014, 18:32:09 UTC | updated ur submodule to 0a399f7 | 27 August 2014, 18:32:09 UTC |
| 9d0dc72 | apregier | 27 August 2014, 18:28:56 UTC | Merge branch 'updated' into gb_master | 27 August 2014, 18:28:56 UTC |
| 5405201 | apregier | 27 August 2014, 18:26:22 UTC | Unescape VEP CSQ field | 27 August 2014, 18:26:22 UTC |
| be629c0 | apregier | 21 August 2014, 15:51:22 UTC | Fasta reporter | 27 August 2014, 18:18:20 UTC |
| c99f50a | Nathaniel Nutter | 27 August 2014, 18:03:27 UTC | updated exepcted XML c6c8aac bumped the memory reservation which showed up in the expected output. | 27 August 2014, 18:03:27 UTC |
| 5b0dbd9 | Jason Walker | 27 August 2014, 17:42:27 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 August 2014, 17:42:27 UTC |
| f72dc9f | Jason Walker | 27 August 2014, 17:42:23 UTC | Add newline to report YAML for indels | 27 August 2014, 17:42:23 UTC |
| abad278 | Thomas Mooney | 27 August 2014, 17:40:33 UTC | Add accessor sub to get target_region_set FeatureList. | 27 August 2014, 17:40:33 UTC |
| c6c8aac | Jason Walker | 27 August 2014, 17:34:33 UTC | Increase RAM for VEP to 32GB from 16GB | 27 August 2014, 17:34:33 UTC |
| 64e5cd9 | Jason Walker | 27 August 2014, 17:33:50 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 August 2014, 17:33:50 UTC |
| b85a690 | Jason Walker | 27 August 2014, 17:33:44 UTC | Remove coverage-vaf and genotype-vaf as required interpreters from VcfReporter | 27 August 2014, 17:33:44 UTC |
| 82c32e9 | Ian Ferguson | 26 August 2014, 20:24:41 UTC | VCF v25: Fix appending FT field in Vcf::VcfFilter | 27 August 2014, 17:24:05 UTC |
| 969bb75 | Jason Walker | 27 August 2014, 17:04:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 August 2014, 17:04:13 UTC |
| 58a92b1 | Jason Walker | 27 August 2014, 17:04:01 UTC | Add a basic version of the CLE report plans which performs no hard filters. | 27 August 2014, 17:04:01 UTC |
| aefd35b | Jason Walker | 27 August 2014, 16:10:23 UTC | Update the name of the plan file used. To start, we need to run without hard filters. | 27 August 2014, 16:10:23 UTC |
| 0b1e8df | Jason Walker | 27 August 2014, 15:25:43 UTC | update the staging dir path again | 27 August 2014, 15:25:43 UTC |
| 10227e2 | Jason Walker | 27 August 2014, 15:20:47 UTC | update the staging dir path as to not conflict with the chimerascan temp directory path when rsyncd | 27 August 2014, 15:20:47 UTC |
| 73a8a70 | Thomas Mooney | 27 August 2014, 13:39:07 UTC | Re-enable somval testcase with a test model. | 27 August 2014, 13:39:07 UTC |
| e177f83 | Thomas Mooney | 27 August 2014, 13:33:17 UTC | Replace production model with test-factory version. | 27 August 2014, 13:33:17 UTC |
| e4643b4 | Thomas Mooney | 27 August 2014, 13:16:19 UTC | whitespace | 27 August 2014, 13:16:19 UTC |
| baeb2e0 | Thomas Mooney | 26 August 2014, 21:23:48 UTC | Updates to handle chromosome names with special characters. | 27 August 2014, 12:54:28 UTC |
| d1e900b | Veena Bhonagiri | 27 August 2014, 12:42:16 UTC | Added model files for P. miyazakii | 27 August 2014, 12:42:16 UTC |
| ee878fd | APipe Tester | 27 August 2014, 12:17:37 UTC | Updated `gmt` tab completion. | 27 August 2014, 12:17:37 UTC |
| 6862e06 | APipe Tester | 27 August 2014, 12:16:55 UTC | Updated `genome` tab completion. | 27 August 2014, 12:16:55 UTC |
| 6f681cd | APipe Tester | 27 August 2014, 12:15:18 UTC | Updated class browser cache. | 27 August 2014, 12:15:18 UTC |
| fd402f6 | Nathaniel Nutter | 27 August 2014, 01:02:33 UTC | instrument query_tcga_barcode so we can tune timeout, sleep, and attempts | 27 August 2014, 01:02:33 UTC |
| 327caf6 | Nathaniel Nutter | 26 August 2014, 22:08:00 UTC | instrument attempts and failures | 27 August 2014, 01:02:02 UTC |
| ba02818 | Nathaniel Nutter | 26 August 2014, 22:07:15 UTC | extract prefix for reuse | 27 August 2014, 01:02:01 UTC |
| a79c4af | Nathaniel Nutter | 26 August 2014, 21:54:04 UTC | return successful attempt number | 27 August 2014, 01:02:00 UTC |
| 3c32192 | Nathaniel Nutter | 26 August 2014, 21:44:31 UTC | add timer instrumentation around query_tcga_barcode request | 27 August 2014, 01:01:59 UTC |
| a103acb | Nathaniel Nutter | 26 August 2014, 21:36:25 UTC | generalize retry_request to just retry I would like to add metrics around query_tcga_barcode and I think a more generalized retry helps facilitate that. | 27 August 2014, 01:01:59 UTC |
| 97b54b0 | Nathaniel Nutter | 27 August 2014, 01:01:18 UTC | moved directory Moved directory because it needs to match package name. Updated source_files.with_new_source_files.tsv and source_files.tsv for new path. | 27 August 2014, 01:01:58 UTC |
| 018197d | Eddie Belter | 26 August 2014, 20:50:35 UTC | InstData Reimport: move generate file for reimport to import name space | 26 August 2014, 20:51:08 UTC |
| e6e521a | Eddie Belter | 26 August 2014, 20:48:43 UTC | InstData Reimport: update attrs excluded; allow multiple files per inst data | 26 August 2014, 20:51:08 UTC |
| 22c6e88 | Thomas Mooney | 26 August 2014, 20:32:59 UTC | Break ties by sorting on date_completed | 26 August 2014, 20:32:59 UTC |
| 348b37e | Thomas Mooney | 26 August 2014, 19:44:34 UTC | Fix spelling; change contact e-mail. | 26 August 2014, 19:44:34 UTC |
| 51f336d | Thomas Mooney | 26 August 2014, 19:28:09 UTC | Remove old `gmt snp screen-seq-by-snp-list`. Remove it rather than fix its spelling. | 26 August 2014, 19:28:09 UTC |
| c3a935f | Thomas Mooney | 26 August 2014, 18:52:09 UTC | s/chromosone/chromosome/ | 26 August 2014, 18:52:09 UTC |
| a5f9be4 | Thomas Mooney | 26 August 2014, 13:05:02 UTC | Update clinseq blessed build due to metric change. | 26 August 2014, 13:05:02 UTC |
| 942ad55 | APipe Tester | 26 August 2014, 12:16:45 UTC | Updated `genome` tab completion. | 26 August 2014, 12:16:45 UTC |
| 3c48440 | APipe Tester | 26 August 2014, 12:15:07 UTC | Updated class browser cache. | 26 August 2014, 12:15:07 UTC |
| fa52422 | Nathaniel Nutter | 22 August 2014, 20:33:26 UTC | remove unused imports | 25 August 2014, 20:44:23 UTC |
| d94dbbc | Thomas Mooney | 25 August 2014, 20:30:16 UTC | Update expected test case for metric change to SummarizeBuilds. | 25 August 2014, 20:30:16 UTC |
| adc0fad | Thomas Mooney | 25 August 2014, 20:17:47 UTC | Update ClinSeq SummarizeBuilds to use metrics The file it was reading previously is no longer being stored in all cases (AUE-321) | 25 August 2014, 20:17:47 UTC |
| 0f5841c | Avinash Ramu | 25 August 2014, 19:40:28 UTC | initialize empty df with 6 cols | 25 August 2014, 19:40:57 UTC |
| 0d81918 | Thomas Mooney | 25 August 2014, 18:40:00 UTC | Use different test model for refalign; omit somval test for now. | 25 August 2014, 18:40:00 UTC |
| c224e1d | Eddie Belter | 25 August 2014, 18:20:09 UTC | InstData REfine Reads: known sites is optional for commands as it in in results | 25 August 2014, 18:20:23 UTC |
| 785fbaa | Thomas Mooney | 25 August 2014, 18:11:42 UTC | Update model define expected case since command was redone. | 25 August 2014, 18:11:42 UTC |
| 86488c3 | Thomas Mooney | 25 August 2014, 17:53:56 UTC | Skip comparing directories since there's only one file. We're about to diff it, anyway. | 25 August 2014, 17:53:56 UTC |
| 86dc585 | Thomas Mooney | 25 August 2014, 17:50:24 UTC | Filter possibly variable path to fpkm file when comparing in test. | 25 August 2014, 17:50:24 UTC |
| 8b3b1d8 | Thomas Mooney | 25 August 2014, 17:04:14 UTC | Explicitly return 1 or 0 (so config can use these values). | 25 August 2014, 17:04:14 UTC |
| a387598 | Thomas Mooney | 25 August 2014, 17:01:32 UTC | Add "is_rna" accessor for benefit of configuration. Hide all sorts of trouble with data integrity behind a single boolean! | 25 August 2014, 17:01:32 UTC |
| ab96892 | Thomas Mooney | 25 August 2014, 15:41:34 UTC | Also skip in shortcut() if skipping. | 25 August 2014, 15:41:34 UTC |
| e312055 | Thomas Mooney | 25 August 2014, 15:38:37 UTC | Set a dummy result ID for benefit of legacy workflow. | 25 August 2014, 15:38:37 UTC |
| 795d802 | Thomas Mooney | 25 August 2014, 15:01:39 UTC | Add brief docs for properties for benefits of define command help text | 25 August 2014, 15:01:39 UTC |
| 0303060 | Thomas Mooney | 25 August 2014, 15:00:35 UTC | Move SomVal define command so basic auto-generated one can be used. | 25 August 2014, 15:00:35 UTC |
| a6f4a4d | Susanna Siebert | 25 August 2014, 13:54:40 UTC | reporter for DoCM vcf | 25 August 2014, 13:54:48 UTC |
| 4ffeff4 | APipe Tester | 23 August 2014, 12:16:30 UTC | Updated `genome` tab completion. | 23 August 2014, 12:16:30 UTC |
| fbfb18c | APipe Tester | 23 August 2014, 12:14:54 UTC | Updated class browser cache. | 23 August 2014, 12:14:54 UTC |
| fffb400 | Gabriel Sanderson | 22 August 2014, 20:34:22 UTC | make rnaseq wrapper a command | 22 August 2014, 20:34:22 UTC |
| 26b35fa | Gabriel Sanderson | 21 August 2014, 19:25:06 UTC | Rnaseq wrapper now automatically runs the report. | 22 August 2014, 20:30:05 UTC |
| c99d2cd | Gabriel Sanderson | 21 August 2014, 18:19:46 UTC | RnaSeq wrapper, currently only creates the resource file | 22 August 2014, 20:29:50 UTC |
| 86b36bc | apregier | 22 August 2014, 17:11:03 UTC | Merge branch 'copy' into gb_master | 22 August 2014, 17:11:03 UTC |
| f09f90d | apregier | 22 August 2014, 17:09:15 UTC | Make coverage_models a separate input from models | 22 August 2014, 17:09:56 UTC |
| f13db33 | Susanna Siebert | 22 August 2014, 16:05:13 UTC | cleaned up formatting and usage of data_dir instead of hardcoded paths | 22 August 2014, 16:07:18 UTC |
| 15eac5e | dmorton | 22 August 2014, 15:48:31 UTC | Bless new somatic-variation build A new default version of bam-readcount leads to more accurate calculations of Tumor VAF | 22 August 2014, 15:49:14 UTC |
| ceb3075 | apregier | 22 August 2014, 15:25:43 UTC | Merge branch 'copy' into gb_master | 22 August 2014, 15:25:43 UTC |
| d68391c | apregier | 22 August 2014, 15:12:27 UTC | Change source tags to sample names | 22 August 2014, 15:12:27 UTC |
| c3f52df | apregier | 22 August 2014, 14:54:29 UTC | Merge branch 'copy' into gb_master | 22 August 2014, 14:54:29 UTC |
| a287e30 | apregier | 22 August 2014, 14:45:49 UTC | Add source when combining d0 and d30 reports in wrapper | 22 August 2014, 14:47:17 UTC |
| fc95225 | apregier | 21 August 2014, 21:33:34 UTC | Optionally add a column of source tags to the combined report | 22 August 2014, 14:47:15 UTC |
| 1b8c1bd | apregier | 21 August 2014, 20:19:42 UTC | Combine files with the same headers but in different orders | 22 August 2014, 14:47:10 UTC |
| bb4d054 | Susanna Siebert | 22 August 2014, 13:16:32 UTC | test files needed for Trio test | 22 August 2014, 13:21:13 UTC |
| e81ca2f | Susanna Siebert | 22 August 2014, 13:16:11 UTC | formatting fixes | 22 August 2014, 13:21:13 UTC |
| 3d1a1cc | Susanna Siebert | 21 August 2014, 19:56:13 UTC | move logic for determing filter results for each allele to separate subroutine | 22 August 2014, 13:21:13 UTC |
| 4f130b9 | Susanna Siebert | 21 August 2014, 19:38:39 UTC | rename filter_interpreters to soft_filters | 22 August 2014, 13:21:13 UTC |
| 7356b9a | Susanna Siebert | 21 August 2014, 18:39:23 UTC | new reporter for vcf indel reporting that inherits from the basic vcf reporter | 22 August 2014, 13:21:13 UTC |
| 39cf2e9 | Susanna Siebert | 21 August 2014, 15:52:08 UTC | additional subtests for previously untested subroutines | 22 August 2014, 13:21:13 UTC |
| fef8e12 | Susanna Siebert | 21 August 2014, 15:51:38 UTC | include vcf report in the full CLE report processing plan files | 22 August 2014, 13:21:13 UTC |
| d1540ce | Susanna Siebert | 21 August 2014, 15:50:55 UTC | add vcf_id and vcf_description subroutines | 22 August 2014, 13:21:12 UTC |
| 06be488 | Susanna Siebert | 21 August 2014, 14:20:43 UTC | Restructure for clarity | 22 August 2014, 13:21:12 UTC |
| e6ab9f3 | Susanna Siebert | 21 August 2014, 14:18:41 UTC | Remove is_filter_interpreter subroutine | 22 August 2014, 13:21:12 UTC |
| 408ac03 | Susanna Siebert | 21 August 2014, 14:17:35 UTC | Remove header_is_written property and use $self->header instead | 22 August 2014, 13:21:12 UTC |
| b2a70dc | APipe Tester | 22 August 2014, 12:17:13 UTC | Updated `genome` tab completion. | 22 August 2014, 12:17:13 UTC |
| 71f9478 | APipe Tester | 22 August 2014, 12:15:28 UTC | Updated class browser cache. | 22 August 2014, 12:15:28 UTC |
| 745666d | Feiyu Du | 21 August 2014, 22:10:55 UTC | add homopolymer filter | 21 August 2014, 22:10:55 UTC |
| 5435896 | Thomas Mooney | 21 August 2014, 21:26:50 UTC | Don't require the parameter if we're going to skip. (Ptero wouldn't care if it wasn't set when shortcutting, but legacy Workflow is more stringent.) | 21 August 2014, 21:26:50 UTC |
| 62d61bf | Nathaniel Nutter | 09 July 2014, 20:31:44 UTC | add renamex and movex that throw exceptions | 21 August 2014, 20:57:21 UTC |
| d06fbbc | Nathaniel Nutter | 07 July 2014, 23:07:59 UTC | fix move_file still using File::Copy directly | 21 August 2014, 20:57:18 UTC |
| fdd24b4 | Nathaniel Nutter | 07 July 2014, 23:00:53 UTC | refactor rename to reuse for move We also need to provide an alternative to File::Copy's `move` function (which is a `rename` with a fallback on a `copy`). Note that File::Copy has different permission modes: `cp` preserves permissions while `copy` does not. However, both `mv` and `move` attempt a `rename` which does preserve permissions. | 21 August 2014, 20:57:12 UTC |
| f2143e2 | Thomas Mooney | 21 August 2014, 20:12:37 UTC | Support supplying a directory instead of a BED file. | 21 August 2014, 20:12:37 UTC |
| 1f47d50 | Thomas Mooney | 21 August 2014, 20:08:10 UTC | In order to support alignment-only builds, no longer require annotation. | 21 August 2014, 20:08:10 UTC |
| ebc66b1 | Thomas Mooney | 21 August 2014, 20:07:41 UTC | Skip run if no verifybamid specified in processing-profile. | 21 August 2014, 20:07:41 UTC |
| 5be2db3 | dmorton | 21 August 2014, 19:14:48 UTC | Add test for allows_hard_filters option on reporters | 21 August 2014, 19:38:49 UTC |
| fb9abbd | dmorton | 21 August 2014, 18:43:58 UTC | Implement allows_hard_filters option on reporters | 21 August 2014, 19:27:30 UTC |
| 81088c3 | dmorton | 21 August 2014, 18:34:48 UTC | Extract __interpreter_plan_errors__ method | 21 August 2014, 19:27:30 UTC |
| de9a93d | Thomas Mooney | 21 August 2014, 19:08:00 UTC | Strip CRs from BED files being imported | 21 August 2014, 19:08:00 UTC |
