| 2352c93 | Anthony Brummett | 08 July 2014, 21:49:58 UTC | Convert base chars to upper-case before comparing Model 5babb2f1f9474861abcb2f2ef93948fa died while processing because $reference was a lower-case c and one of the $genotype_alleles was upper-case | 08 July 2014, 23:53:03 UTC |
| 7c44523 | APipe Tester | 08 July 2014, 21:10:51 UTC | updated workflow submodule to 541917f | 08 July 2014, 21:10:51 UTC |
| d8a6cde | Gabriel Sanderson | 08 July 2014, 21:01:03 UTC | Skip assigning instrument data that has already been assigned | 08 July 2014, 21:09:12 UTC |
| 547fdf6 | apregier | 08 July 2014, 19:49:30 UTC | Merge branch 'fireteam' into gb_master | 08 July 2014, 19:49:30 UTC |
| 2b32db3 | apregier | 08 July 2014, 18:47:02 UTC | Add Target file URL field to sdrf | 08 July 2014, 19:46:26 UTC |
| 029ebeb | apregier | 08 July 2014, 18:20:21 UTC | Allow builds without target_region_set_name (WGS) | 08 July 2014, 19:46:23 UTC |
| 76fa2d9 | Susanna Siebert | 08 July 2014, 18:56:54 UTC | bump test versions for Genome::VariantReporting::Framework::Command::AnnotateBuild | 08 July 2014, 18:58:49 UTC |
| 84b0296 | Gabriel Sanderson | 08 July 2014, 18:45:03 UTC | Updated plan to work with simple report changes | 08 July 2014, 18:45:03 UTC |
| 08f4050 | Susanna Siebert | 08 July 2014, 18:21:33 UTC | bump test data version | 08 July 2014, 18:21:33 UTC |
| 803c552 | Susanna Siebert | 08 July 2014, 18:07:30 UTC | add lsf resource parameter to Vep because it regularly runs out of memory for indel files | 08 July 2014, 18:08:21 UTC |
| aa174f7 | Susanna Siebert | 08 July 2014, 18:06:49 UTC | handle entries with no bam readcount information | 08 July 2014, 18:08:20 UTC |
| 7a48a44 | Susanna Siebert | 08 July 2014, 18:06:20 UTC | handle bam readcount and coverage of 0 | 08 July 2014, 18:08:19 UTC |
| c8fef1b | Susanna Siebert | 08 July 2014, 15:24:37 UTC | updated simple reporter and plan files for CLE testing | 08 July 2014, 18:08:19 UTC |
| 0a3578b | Susanna Siebert | 08 July 2014, 15:03:17 UTC | new interpreter to output info tags of an entry | 08 July 2014, 18:08:18 UTC |
| 66b74f3 | Susanna Siebert | 08 July 2014, 15:02:21 UTC | new interpreter to output whether variant is homozygous or heterozygous | 08 July 2014, 18:08:17 UTC |
| 0838fec | Jason Walker | 08 July 2014, 17:28:41 UTC | When deciding which FPKM value to report for duplicate gene_ids, handle na values to avoid numeric errors. | 08 July 2014, 17:28:41 UTC |
| d885468 | Jason Walker | 08 July 2014, 16:02:51 UTC | initial commit of CoverageStatsSummary. This command will be used to summarize the coverage metrics for all somatic valiation models given. | 08 July 2014, 16:02:51 UTC |
| 060bd9f | Feiyu Du | 08 July 2014, 14:27:34 UTC | add paired_end check to make sure the paired_end status | 08 July 2014, 14:27:34 UTC |
| 2792e25 | APipe Tester | 07 July 2014, 23:21:15 UTC | updated graphite submodule to 4370771 | 07 July 2014, 23:21:15 UTC |
| 07cac17 | APipe Tester | 07 July 2014, 22:42:46 UTC | updated graphite submodule to 8bf345a | 07 July 2014, 22:42:46 UTC |
| 4342634 | Travis Abbott | 01 July 2014, 17:44:59 UTC | remove unused params | 07 July 2014, 19:42:46 UTC |
| 43a7090 | Travis Abbott | 23 June 2014, 16:26:48 UTC | add itx processing to breakdancer-to-bed | 07 July 2014, 19:42:46 UTC |
| 347c969 | dmorton | 07 July 2014, 02:25:22 UTC | File::Vcf::Differ can return HeaderDiff objects | 07 July 2014, 02:53:57 UTC |
| 5abc0f5 | dmorton | 07 July 2014, 02:41:24 UTC | Revert "VariantReporting subsystem works on files not just builds" This reverts commit 8b86f4b7be8e3bf9407af93651f2f365ee54ba37. | 07 July 2014, 02:41:24 UTC |
| b597494 | dmorton | 07 July 2014, 02:41:09 UTC | Revert "remove wait statement from test" This reverts commit 509dda8a376f901b0252728981c7d967574271da. | 07 July 2014, 02:41:09 UTC |
| 3426ab6 | dmorton | 07 July 2014, 02:40:57 UTC | Revert "VariantReporting Expert Commands shortcut properly" This reverts commit eddd5b567c8de9d25170f811dbad61703ab3b50e. | 07 July 2014, 02:40:57 UTC |
| eddd5b5 | dmorton | 05 July 2014, 20:06:47 UTC | VariantReporting Expert Commands shortcut properly Properties that are considered 'paths' are hashed with the md5 algorithm and that value is used to shortcut/produce software-results. | 05 July 2014, 20:06:47 UTC |
| 509dda8 | dmorton | 05 July 2014, 20:06:27 UTC | remove wait statement from test | 05 July 2014, 20:06:27 UTC |
| 8b86f4b | dmorton | 02 July 2014, 17:21:59 UTC | VariantReporting subsystem works on files not just builds The ResourceProvider replaces the build, at least conceptually. Running on a build will consist of generating a ResourceProvider first, and then running the subsystem. This commit is a regression in that sense, because running on a build has been disabled for now. The ReportGeneratorWrapper goes away entirely, since translations can be provided by the ResourceProvider. Expert commands accept files instead of objects for the most part, and when they need objects from the ResourceProvider, they are given ids only. | 05 July 2014, 17:47:33 UTC |
| a985eeb | dmorton | 02 July 2014, 17:20:42 UTC | Split __planned_output_errors__ into two parts | 05 July 2014, 17:47:33 UTC |
| f70e46a | dmorton | 03 July 2014, 19:37:32 UTC | Extract method 'hash_repr' and 'columns_for_header' | 05 July 2014, 17:47:32 UTC |
| 9c892e1 | APipe Tester | 03 July 2014, 19:39:02 UTC | updated ur submodule to 2c4ed48 | 03 July 2014, 20:56:48 UTC |
| cd2c701 | Gabriel Sanderson | 03 July 2014, 19:33:16 UTC | Added per_library_vaf to the interpreter. | 03 July 2014, 19:42:24 UTC |
| 096dad4 | Gabriel Sanderson | 03 July 2014, 19:04:21 UTC | Add more test output | 03 July 2014, 19:42:24 UTC |
| ee4c84b | Gabriel Sanderson | 03 July 2014, 18:59:17 UTC | Make per_lib vaf calculation method. Refactor total vaf method to use it. | 03 July 2014, 19:42:23 UTC |
| 4e16283 | Gabriel Sanderson | 02 July 2014, 23:17:55 UTC | Add calculate_per_library_vaf, which calculate_vaf calls | 03 July 2014, 19:42:23 UTC |
| 48203d7 | Gabriel Sanderson | 02 July 2014, 23:05:26 UTC | calculate_coverage_for_allele now just sums the per_library version | 03 July 2014, 19:42:22 UTC |
| 9d6be79 | Gabriel Sanderson | 02 July 2014, 21:27:16 UTC | Add per_library_ref_count | 03 July 2014, 19:42:21 UTC |
| 1ce61e0 | Gabriel Sanderson | 02 July 2014, 20:40:59 UTC | Slight refactor when calling per_library_coverage | 03 July 2014, 19:42:21 UTC |
| 2381763 | Gabriel Sanderson | 01 July 2014, 21:53:42 UTC | Add per_library_var_count tests for indels | 03 July 2014, 19:42:20 UTC |
| 88ff0e8 | Gabriel Sanderson | 01 July 2014, 21:50:55 UTC | Added per_library_var_count to VafInterpreter | 03 July 2014, 19:42:20 UTC |
| abc8447 | Gabriel Sanderson | 01 July 2014, 21:31:02 UTC | refactor out per library coverage | 03 July 2014, 19:42:19 UTC |
| a00201f | Gabriel Sanderson | 01 July 2014, 21:21:00 UTC | refactor logic to a method for translating the reference | 03 July 2014, 19:42:18 UTC |
| 932d474 | Avinash Ramu | 03 July 2014, 16:26:16 UTC | update clinseq blessed | 03 July 2014, 16:26:16 UTC |
| 2cd77fe | Avinash Ramu | 02 July 2014, 22:06:26 UTC | get variant sources stats | 03 July 2014, 15:19:22 UTC |
| 5ec015f | Avinash Ramu | 02 July 2014, 22:05:38 UTC | get SV type stats | 03 July 2014, 15:19:21 UTC |
| ad147d7 | Avinash Ramu | 02 July 2014, 17:30:40 UTC | refactor3 | 03 July 2014, 15:19:20 UTC |
| 6d8fbe5 | Avinash Ramu | 02 July 2014, 17:09:14 UTC | refactor2 | 03 July 2014, 15:19:20 UTC |
| 683bd8b | Avinash Ramu | 02 July 2014, 16:19:48 UTC | remove whitespace | 03 July 2014, 15:19:19 UTC |
| 9979c19 | Avinash Ramu | 02 July 2014, 16:18:33 UTC | refactor1 | 03 July 2014, 15:19:19 UTC |
| ea4bd17 | APipe Tester | 03 July 2014, 12:21:06 UTC | Updated `genome` tab completion. | 03 July 2014, 12:21:06 UTC |
| 9f75b45 | APipe Tester | 03 July 2014, 12:18:46 UTC | Updated class browser cache. | 03 July 2014, 12:18:46 UTC |
| 26783f4 | APipe Tester | 03 July 2014, 00:01:03 UTC | updated graphite submodule to d587278 | 03 July 2014, 00:01:03 UTC |
| 1740940 | APipe Tester | 02 July 2014, 22:57:59 UTC | updated graphite submodule to 9461b68 | 02 July 2014, 22:57:59 UTC |
| 0dc8171 | Eddie Belter | 02 July 2014, 21:40:17 UTC | Revert "InsData Import: renmae tcga bam test" This reverts commit 8b5654c3506a241a7d1e8441ced7307d132a9fd8. | 02 July 2014, 21:41:36 UTC |
| bad0f6b | Eddie Belter | 02 July 2014, 21:26:59 UTC | InstData Import: spelling errors | 02 July 2014, 21:41:36 UTC |
| 76bded5 | Eddie Belter | 02 July 2014, 21:04:56 UTC | InstData Import: tcga load metadata | 02 July 2014, 21:41:35 UTC |
| c507170 | Eddie Belter | 26 June 2014, 19:42:40 UTC | InstData Import: remove all auxillary files for path; update tests to check for all files | 02 July 2014, 21:41:35 UTC |
| 832f1ed | Eddie Belter | 26 June 2014, 19:33:35 UTC | InstData Import: get md5 and orig md5 paths to helpers | 02 July 2014, 21:41:34 UTC |
| 9288363 | Eddie Belter | 26 June 2014, 18:31:44 UTC | InstData Import: clean up verify md5 | 02 July 2014, 21:41:34 UTC |
| b520678 | Eddie Belter | 26 June 2014, 18:15:25 UTC | InstData Import: rename method to check if md5s previously imported | 02 July 2014, 21:41:33 UTC |
| 2825a96 | Eddie Belter | 26 June 2014, 18:05:29 UTC | InsData Import: renmae tcga bam test | 02 July 2014, 21:41:32 UTC |
| 2d0694f | Eddie Belter | 24 June 2014, 22:01:09 UTC | InstData Import: rm unused importer for complete genomics | 02 July 2014, 21:41:30 UTC |
| 2654af1 | Susanna Siebert | 02 July 2014, 20:46:23 UTC | new interpreter to output the size of indels | 02 July 2014, 20:46:23 UTC |
| bfcbd1e | Susanna Siebert | 02 July 2014, 20:42:31 UTC | new interpreter to output the bamreadcount coverage | 02 July 2014, 20:42:31 UTC |
| c207ac3 | Susanna Siebert | 02 July 2014, 20:41:57 UTC | fixed some missing renamings from filter to interpreter | 02 July 2014, 20:41:57 UTC |
| c5087ac | Susanna Siebert | 02 July 2014, 20:17:38 UTC | interpreter to output the value of the FT field | 02 July 2014, 20:29:40 UTC |
| 15028de | Susanna Siebert | 02 July 2014, 20:15:34 UTC | renamed filter to max-indel-size also fixed some spelling errors | 02 July 2014, 20:29:38 UTC |
| c87cd76 | Susanna Siebert | 02 July 2014, 20:14:03 UTC | Custom interpret_entry method (mainly to provide a custom header) | 02 July 2014, 20:29:38 UTC |
| 05e7414 | Susanna Siebert | 02 July 2014, 20:13:07 UTC | Bugfix: parameters weren't passed in correctly | 02 July 2014, 20:29:37 UTC |
| fa29ab8 | Eddie Belter | 02 July 2014, 20:26:30 UTC | InstData Reimport: generate file for reimport param file defaults to STDOUT | 02 July 2014, 20:26:41 UTC |
| 8820823 | Thomas Mooney | 02 July 2014, 20:18:03 UTC | Add accessor through to processing profile param for LOH strategy. | 02 July 2014, 20:18:03 UTC |
| cde1301 | Thomas Mooney | 02 July 2014, 20:12:13 UTC | Only look for LOH result if we had the strategy to create one. | 02 July 2014, 20:12:13 UTC |
| cc76af4 | dmorton | 05 June 2014, 19:55:36 UTC | Change location of Hgmi installation directory | 02 July 2014, 18:30:44 UTC |
| 9f552e5 | Eddie Belter | 02 July 2014, 17:46:45 UTC | InstData Reimport: support to update source files when generating reimport source files tsv | 02 July 2014, 17:48:15 UTC |
| 41e562c | Gabriel Sanderson | 02 July 2014, 17:12:56 UTC | Updated acmg gene set | 02 July 2014, 17:12:56 UTC |
| 4384a5a | Eddie Belter | 02 July 2014, 16:12:38 UTC | InstData reimport: move getting attrs for reimport from comand to reimport module | 02 July 2014, 16:19:53 UTC |
| 76ca381 | Nathaniel Nutter | 02 July 2014, 02:17:26 UTC | improvements to PSGI apps | 02 July 2014, 02:17:26 UTC |
| 26efcdf | Nathaniel Nutter | 02 July 2014, 02:16:05 UTC | set --env so Plack::Runner doesn't enable its own dev middleware | 02 July 2014, 02:16:05 UTC |
| e2a9c80 | Nathaniel Nutter | 02 July 2014, 01:54:13 UTC | add timezone to timestamp | 02 July 2014, 01:54:13 UTC |
| 32ef730 | Nathaniel Nutter | 01 July 2014, 20:08:51 UTC | update hard-coded restart command | 01 July 2014, 21:03:07 UTC |
| d77ebfa | Nathaniel Nutter | 01 July 2014, 20:03:13 UTC | restore Lint and StackTrace middleware for dev server | 01 July 2014, 21:03:06 UTC |
| f1ee5cf | Nathaniel Nutter | 01 July 2014, 19:56:40 UTC | enable access log middleware for dev server | 01 July 2014, 21:03:04 UTC |
| 444d9e3 | Nathaniel Nutter | 01 July 2014, 19:55:27 UTC | this middleware needs to wrap Main.psgi not each child app | 01 July 2014, 21:03:03 UTC |
| 7b93381 | Nathaniel Nutter | 01 July 2014, 19:39:56 UTC | whitespace | 01 July 2014, 21:03:01 UTC |
| 7490e6d | dmorton | 01 July 2014, 18:42:20 UTC | Move Interpreter::Fpkm to Fpkm::EntryParser | 01 July 2014, 18:53:21 UTC |
| a9f599b | Thomas Mooney | 01 July 2014, 18:49:08 UTC | Purge and set test name on results when expunging. Previously they would be deleted outright which eliminates tracking of past processing. (This also provides our standard undo from the trash volumes.) | 01 July 2014, 18:49:08 UTC |
| 285a79c | Thomas Mooney | 01 July 2014, 18:48:00 UTC | Don't force build abandonment just because of model input changes. | 01 July 2014, 18:48:00 UTC |
| 94fc951 | Susanna Siebert | 01 July 2014, 18:23:59 UTC | allow "normal" samples in the list of translations | 01 July 2014, 18:23:59 UTC |
| 6f7b870 | Gabriel Sanderson | 01 July 2014, 17:34:51 UTC | use Set::Scalar. Rename to gene_set. | 01 July 2014, 17:37:20 UTC |
| 46e11eb | Feiyu Du | 01 July 2014, 17:35:28 UTC | 1. Modified Downsample.pm to work better and correctly 2. modified AdspExomeQcSummary.pm with updated alignment metrics | 01 July 2014, 17:35:28 UTC |
| bf20fcb | Chris Miller | 01 July 2014, 16:58:57 UTC | making header matching a bit more flexible | 01 July 2014, 16:59:18 UTC |
| 51803b2 | Chris Miller | 17 June 2014, 20:22:56 UTC | adding traceback option, which should aid debugging a little bit | 01 July 2014, 16:59:17 UTC |
| 85566dd | dmorton | 01 July 2014, 15:57:38 UTC | Move Filter/GeneFilter to Vep | 01 July 2014, 15:57:38 UTC |
| d978fb2 | dmorton | 30 June 2014, 23:06:20 UTC | Move VariantReporting::Plan to Framework::Plan::MasterPlan | 01 July 2014, 14:36:39 UTC |
| 93bfe3a | dmorton | 30 June 2014, 22:59:18 UTC | Move Plan to Framework | 01 July 2014, 14:36:39 UTC |
| b15f9db | dmorton | 30 June 2014, 22:57:15 UTC | Move Component to Framework | 01 July 2014, 14:36:39 UTC |
| d79fa7f | dmorton | 30 June 2014, 22:54:55 UTC | Move GetInitialVcfResult.pm to Framework | 01 July 2014, 14:36:39 UTC |
| c20dad3 | dmorton | 30 June 2014, 22:52:31 UTC | Move Common::Dag to Framework | 01 July 2014, 14:36:33 UTC |
| 84cbacc | dmorton | 30 June 2014, 22:50:02 UTC | Move ReportGenerator to Framework | 01 July 2014, 14:36:33 UTC |
