| 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 |
| 63db3d0 | Gabriel Sanderson | 21 August 2014, 16:51:35 UTC | Merge branch 'vcf-info-strings' | 21 August 2014, 16:51:35 UTC |
| 915be1f | APipe Tester | 21 August 2014, 12:16:49 UTC | Updated `genome` tab completion. | 21 August 2014, 12:16:49 UTC |
| e3106c0 | APipe Tester | 21 August 2014, 12:15:15 UTC | Updated class browser cache. | 21 August 2014, 12:15:15 UTC |
| 70bee8a | Eddie Belter | 20 August 2014, 23:43:34 UTC | InstData Import: add insert extension to bam path to Helpers | 20 August 2014, 23:43:53 UTC |
| 11f2deb | Ian Ferguson | 20 August 2014, 22:29:53 UTC | Escape --intervals args in GMT::Mutect shell cmd | 20 August 2014, 22:35:04 UTC |
| f17efe6 | Eddie Belter | 20 August 2014, 17:45:06 UTC | InstData: rm microarray command tree | 20 August 2014, 22:31:28 UTC |
| 31dd6ed | Eddie Belter | 01 August 2014, 19:36:40 UTC | InstData Import: tcga bam test no longer decrements the dummy id | 20 August 2014, 22:31:28 UTC |
| 9838346 | Eddie Belter | 01 August 2014, 19:35:14 UTC | InstData Import: tcga bam no longer test model is created | 20 August 2014, 22:31:27 UTC |
| 23bd608 | dmorton | 20 August 2014, 21:38:55 UTC | Add input_a and input_b properties | 20 August 2014, 22:29:56 UTC |
| c5af00e | dmorton | 20 August 2014, 20:16:55 UTC | Ensure that the previous_result shares the test_name of this result This is when looking up the previous_result from the current_result. | 20 August 2014, 22:29:56 UTC |
| 720d9aa | dmorton | 20 August 2014, 20:15:52 UTC | Use the previous results test_name It is an error if the previous_result could have a different test name from the current result. | 20 August 2014, 22:29:56 UTC |
| 09145b1 | dmorton | 20 August 2014, 18:00:20 UTC | Don't look for vcf results when there aren't any Combine results whose input results did not both make a vcf result don't have an associated vcf result of their own. | 20 August 2014, 22:29:56 UTC |
| 74715d5 | dmorton | 20 August 2014, 17:59:13 UTC | Use the same test_name as the DV2 result Instead of relying on the environment variable to be the same as it was when the result was generated, we use the same test_name as that result when looking for the associated vcf-result | 20 August 2014, 22:29:56 UTC |
| 50351ed | Thomas Mooney | 20 August 2014, 22:24:03 UTC | s/instrumetn/instrument/ | 20 August 2014, 22:24:03 UTC |
| 13a1b4e | Thomas Mooney | 20 August 2014, 22:05:23 UTC | s/ teh / the /g | 20 August 2014, 22:05:23 UTC |
| f6b48bc | Thomas Mooney | 20 August 2014, 22:03:33 UTC | s/ adn / and /g | 20 August 2014, 22:03:33 UTC |
| 64cb7e5 | Thomas Mooney | 20 August 2014, 21:59:47 UTC | Fix spelling of "allocation" | 20 August 2014, 21:59:47 UTC |
| 43ecb7b | Thomas Mooney | 20 August 2014, 21:57:01 UTC | s/eror/error/ | 20 August 2014, 21:57:01 UTC |
| 5198783 | Thomas Mooney | 20 August 2014, 21:51:36 UTC | s/ ot / to /g | 20 August 2014, 21:51:36 UTC |
| 1a59ebb | Thomas Mooney | 20 August 2014, 21:49:51 UTC | s/buid ot/build to/ | 20 August 2014, 21:49:51 UTC |
| ffebd11 | Thomas Mooney | 20 August 2014, 21:47:26 UTC | s/succeded/succeeded/g | 20 August 2014, 21:47:26 UTC |
| 20df7bc | Thomas Mooney | 20 August 2014, 21:46:20 UTC | Fix typo "suceed" => "succeeded" | 20 August 2014, 21:46:20 UTC |
| 8ddbd6f | Thomas Mooney | 20 August 2014, 21:42:17 UTC | Fill in a brief help_detail since help_brief doesn't appear in --help | 20 August 2014, 21:42:17 UTC |
| 965953d | Thomas Mooney | 20 August 2014, 21:39:41 UTC | Add a doc line for --model. | 20 August 2014, 21:39:41 UTC |
| 9096382 | Thomas Mooney | 20 August 2014, 21:37:55 UTC | s/compatable/compatible/g | 20 August 2014, 21:37:55 UTC |
| 2b82646 | Thomas Mooney | 20 August 2014, 21:30:03 UTC | Update somval model naming to prefer the "tumor_sample" information. | 20 August 2014, 21:30:03 UTC |
| 99047c5 | apregier | 20 August 2014, 20:31:18 UTC | Merge branch 'copy' into gb_master | 20 August 2014, 20:31:18 UTC |
| 6118e27 | apregier | 20 August 2014, 20:29:25 UTC | Use new enforce-equal-unordered for seg-dup field | 20 August 2014, 20:30:14 UTC |
| e60c88f | Thomas Mooney | 20 August 2014, 20:28:38 UTC | Remove unused option "auto_increment". | 20 August 2014, 20:28:38 UTC |
| 40f3489 | Jim Weible | 20 August 2014, 19:30:22 UTC | require an instrument data and a merged alignment result so this does something that makes slightly more sense | 20 August 2014, 19:30:22 UTC |
| 79033da | Jim Weible | 20 August 2014, 18:57:38 UTC | basic index illumina replacement | 20 August 2014, 18:57:48 UTC |
| a9a3689 | apregier | 20 August 2014, 18:43:59 UTC | Use set_info_field inside add_allele | 20 August 2014, 18:43:59 UTC |
| dfdc6ab | Susanna Siebert | 20 August 2014, 18:36:36 UTC | Merge branch 'variant_reporting_simple_vcf' | 20 August 2014, 18:36:36 UTC |
| 8f3af63 | Susanna Siebert | 20 August 2014, 18:25:12 UTC | test for VcfReporter | 20 August 2014, 18:25:12 UTC |
| 8a705c0 | Susanna Siebert | 20 August 2014, 18:24:39 UTC | minor refactor to make testing easier | 20 August 2014, 18:24:39 UTC |
| 7e6ef3c | Thomas Mooney | 20 August 2014, 17:46:37 UTC | Use generic attribute hint instead of hinting each individual attribute. This reduces the complexity of the underlying SQL to a single JOIN for all attributes instead of one per requested attribute. (In testing this shaved four seconds from a commonly-used query in ClinSeq.) | 20 August 2014, 17:46:37 UTC |
| a5bdf09 | apregier | 20 August 2014, 17:13:29 UTC | Merge branch 'copy' into gb_master | 20 August 2014, 17:13:29 UTC |
| 4db4deb | apregier | 20 August 2014, 16:09:48 UTC | Extract method to calculate new line | 20 August 2014, 17:10:33 UTC |
| dc8dfe0 | apregier | 20 August 2014, 16:05:27 UTC | Extract calculate new header method | 20 August 2014, 17:10:32 UTC |
| 4411386 | apregier | 20 August 2014, 16:02:10 UTC | Extract get_keys_to_append method | 20 August 2014, 17:10:32 UTC |
| 13e034b | apregier | 20 August 2014, 15:56:48 UTC | Use get_header subroutine | 20 August 2014, 17:10:31 UTC |
