| b4bdb76 | Eddie Belter | 25 September 2013, 16:40:24 UTC | Library: add trancript strand | 25 September 2013, 16:51:52 UTC |
| 3060e7c | APipe Tester | 25 September 2013, 04:03:39 UTC | Updated `gmt` tab completion. | 25 September 2013, 04:03:39 UTC |
| d5e2ad0 | APipe Tester | 25 September 2013, 04:02:33 UTC | Updated `genome` tab completion. | 25 September 2013, 04:02:33 UTC |
| d449964 | APipe Tester | 25 September 2013, 04:00:09 UTC | Updated class browser cache. | 25 September 2013, 04:00:09 UTC |
| afb0bcd | Chris Miller | 25 September 2013, 03:50:32 UTC | reverting changes until new R package version is deployed | 25 September 2013, 03:50:49 UTC |
| a5d0a37 | APipe Tester | 25 September 2013, 02:12:09 UTC | Updated `gmt` tab completion. | 25 September 2013, 02:12:09 UTC |
| e6ad191 | APipe Tester | 25 September 2013, 02:11:06 UTC | Updated `genome` tab completion. | 25 September 2013, 02:11:06 UTC |
| bc11911 | APipe Tester | 25 September 2013, 02:09:05 UTC | Updated class browser cache. | 25 September 2013, 02:09:05 UTC |
| 508924d | Chris Miller | 25 September 2013, 01:21:41 UTC | updating tiering sanity checks and adding option to filter review by status | 25 September 2013, 01:22:03 UTC |
| 43329ec | Chris Miller | 25 September 2013, 01:19:49 UTC | adding tumor-purity option | 25 September 2013, 01:22:01 UTC |
| 3cbf160 | APipe Tester | 25 September 2013, 00:18:46 UTC | Updated `genome` tab completion. | 25 September 2013, 00:18:46 UTC |
| 951a3f5 | APipe Tester | 25 September 2013, 00:16:51 UTC | Updated class browser cache. | 25 September 2013, 00:16:51 UTC |
| 9405463 | apregier | 24 September 2013, 21:25:08 UTC | Importer for cosmic imported variation build with vcf | 24 September 2013, 21:30:19 UTC |
| 6d3bc44 | Feiyu Du | 24 September 2013, 20:09:14 UTC | add ensembl transcript id to filter output | 24 September 2013, 20:10:57 UTC |
| bb70cb4 | Thomas Mooney | 24 September 2013, 19:50:23 UTC | Updated the gene-prediction bacterial blessed build | 24 September 2013, 19:50:23 UTC |
| c1e7c00 | APipe Tester | 24 September 2013, 17:59:14 UTC | Updated `gmt` tab completion. | 24 September 2013, 17:59:14 UTC |
| c855235 | APipe Tester | 24 September 2013, 17:58:04 UTC | Updated `genome` tab completion. | 24 September 2013, 17:58:04 UTC |
| 15a7073 | APipe Tester | 24 September 2013, 17:56:04 UTC | Updated class browser cache. | 24 September 2013, 17:56:04 UTC |
| 6d123a1 | Feiyu Du | 24 September 2013, 17:17:50 UTC | Make chimera-scan command | 24 September 2013, 17:19:40 UTC |
| 37ba88f | Feiyu Du | 24 September 2013, 17:17:10 UTC | Make filteroutput outout bed format | 24 September 2013, 17:19:40 UTC |
| 8524f55 | apregier | 24 September 2013, 15:08:38 UTC | Don't die if gene list is empty | 24 September 2013, 15:09:05 UTC |
| 313430f | Eddie Belter | 23 September 2013, 22:24:44 UTC | SomVal/Inst Data composite: accept refiner known sites as many | 23 September 2013, 22:32:24 UTC |
| c711b4c | APipe Tester | 23 September 2013, 20:58:41 UTC | Updated `gmt` tab completion. | 23 September 2013, 20:58:41 UTC |
| cf713b5 | APipe Tester | 23 September 2013, 20:57:51 UTC | Updated `genome` tab completion. | 23 September 2013, 20:57:51 UTC |
| 57becf0 | APipe Tester | 23 September 2013, 20:55:46 UTC | Updated class browser cache. | 23 September 2013, 20:55:46 UTC |
| 65ac0b7 | dmorton | 23 September 2013, 19:25:34 UTC | Merge CreateCrossSampleVcf for indels | 23 September 2013, 19:25:34 UTC |
| 545792f | dmorton | 23 September 2013, 18:56:21 UTC | Diff vcf files without regard to sample order. | 23 September 2013, 19:24:52 UTC |
| 573c892 | dmorton | 23 September 2013, 18:54:01 UTC | Added Genome::File::Vcf::Differ It will diff vcf files without regard to sample order. | 23 September 2013, 19:24:51 UTC |
| fdf5819 | dmorton | 23 September 2013, 14:54:47 UTC | Tests no longer rely on database entities Except of course for the reference sequence build. | 23 September 2013, 19:24:51 UTC |
| 6cbc7a0 | dmorton | 23 September 2013, 14:35:38 UTC | Remove build subclass restriction We now check that the build follows an api via genome model build validate. | 23 September 2013, 19:24:51 UTC |
| e861978 | dmorton | 20 September 2013, 18:53:49 UTC | Working indels and snvs test for ccsvcf | 23 September 2013, 19:24:50 UTC |
| f945491 | dmorton | 20 September 2013, 18:12:54 UTC | Add exact_pos to indel final merge Since it is only available in joinx 1.7, bump the default to that. | 23 September 2013, 19:24:50 UTC |
| 50d6f03 | dmorton | 20 September 2013, 18:10:01 UTC | Add exact_pos option to gmt joinx vcf-merge | 23 September 2013, 19:24:50 UTC |
| 250bcf7 | dmorton | 20 September 2013, 17:37:38 UTC | Don't allow labeled-input-files in safe-vcf-merge | 23 September 2013, 19:24:50 UTC |
| 365fa35 | dmorton | 20 September 2013, 17:30:34 UTC | Programmatically gather inherited Joinx properties Instead of hard-coding them. This lets people add to VcfMerge and SafeVcfMerge still just works as expected. We ignore the is_many properties because they only refer to the inputs which we're going put into batches. | 23 September 2013, 19:24:49 UTC |
| 1b9e2b2 | dmorton | 19 September 2013, 21:17:59 UTC | Final vcf merge has 'merge_samples=1' when processing indels. | 23 September 2013, 19:24:49 UTC |
| b0ad7ff | dmorton | 19 September 2013, 21:14:54 UTC | Fixup indel vcf xml Fix ParallelBy syntax Added different directories for vcf_merging for initial and final Added use_bgzip option to varscan Added merge_samples option to final vcf merge | 23 September 2013, 19:24:49 UTC |
| fbc5a30 | dmorton | 19 September 2013, 21:13:40 UTC | add .gz to varscan output to reflect options provided | 23 September 2013, 19:24:48 UTC |
| cb92423 | dmorton | 19 September 2013, 21:11:32 UTC | Added use_bgzip option to gmt varscan consensus This was for create-cross-sample-vcf with indels work | 23 September 2013, 19:24:48 UTC |
| 8dd829b | dmorton | 19 September 2013, 18:35:41 UTC | Ensure bam file from AnalyzeWindowFile is sorted and indexed gmt varscan consensus is the next step after this is run in the create-cross-sample-vcf workflow for indels. It seems to have trouble unless its inputs are sorted. | 23 September 2013, 19:24:47 UTC |
| 247e1a1 | dmorton | 19 September 2013, 17:40:36 UTC | Ensure max_files_per_merge is being set This was missing from the xml, setting it made it apparent that we need two working directories (one for the initial merge and another for the final merge). | 23 September 2013, 18:57:49 UTC |
| 9a847c4 | dmorton | 19 September 2013, 17:34:40 UTC | use same max_files_per_merge in both tests | 23 September 2013, 18:57:49 UTC |
| f1b4fdd | dmorton | 19 September 2013, 16:24:08 UTC | CreateCrossSampleVcf overhaul for snvs We now use a single workflow xml file with parallelBy so that this will scale with ptero, and so that the snvs and indels code can be shared as much as possible. | 23 September 2013, 18:57:49 UTC |
| 48b193f | dmorton | 19 September 2013, 15:54:06 UTC | Fix typo backfill(ed) | 23 September 2013, 18:57:49 UTC |
| 0def7d0 | dmorton | 19 September 2013, 15:53:02 UTC | Make region file a gzip file and allow case of no alts | 23 September 2013, 18:57:48 UTC |
| d3d3bcb | dmorton | 19 September 2013, 15:52:14 UTC | Fix parallelBy syntax | 23 September 2013, 18:57:48 UTC |
| 7b2d286 | dmorton | 18 September 2013, 20:32:39 UTC | Added get_detectors method to dv2 strategy This allows us to not parse the strategy string by hand in CreateCrossSampleVcf. | 23 September 2013, 18:57:48 UTC |
| 575928b | dmorton | 18 September 2013, 18:19:23 UTC | Added processing_profile option to gmb validate | 23 September 2013, 18:57:48 UTC |
| 3e4b209 | dmorton | 18 September 2013, 00:13:34 UTC | Added RegionLimitVcf to ccsvcf It is just a wrapper around RegionLimit which allows it to take a build as an input. | 23 September 2013, 18:57:48 UTC |
| 57a25cc | dmorton | 18 September 2013, 00:01:44 UTC | Add FIXME | 23 September 2013, 18:57:48 UTC |
| 652a52d | dmorton | 18 September 2013, 00:01:22 UTC | Fix typo | 23 September 2013, 18:57:48 UTC |
| f1311af | dmorton | 18 September 2013, 00:00:39 UTC | Added xml to describe ccsvcf for indels with region limiting | 23 September 2013, 18:57:48 UTC |
| 9b08c04 | dmorton | 17 September 2013, 23:59:58 UTC | Added xml to describe ccsvcf for snvs with region limiting | 23 September 2013, 18:57:48 UTC |
| 59ad94a | dmorton | 17 September 2013, 23:58:03 UTC | Add Pileup and Backfill to ccsvcf These commands just wrap some other gmt commands so they can take 'build_clump's as inputs. They're used in the BackfillVcf step of create-crosss-sample-vcf for snvs. | 23 September 2013, 18:57:47 UTC |
| 8e58c55 | dmorton | 17 September 2013, 23:56:50 UTC | Add CreateRegionFile to ccsvcf This lets us only convert the segregating_sites_vcf_file one time before the parallel-by BackfillVcf step. | 23 September 2013, 18:57:47 UTC |
| b2d7e77 | Gabriel Sanderson | 17 September 2013, 17:35:09 UTC | work so far! | 23 September 2013, 18:57:47 UTC |
| 291a411 | Gabriel Sanderson | 16 September 2013, 19:43:07 UTC | First pass top-down work, mostly from Friday. Simplify generate_result. Move all validation to one method. Move all workflow input generation to one method. Use Build clumps. | 23 September 2013, 18:57:47 UTC |
| 47f4c52 | Gabriel Sanderson | 17 September 2013, 17:35:28 UTC | remove unnecessary module | 23 September 2013, 18:57:47 UTC |
| 0f05215 | Gabriel Sanderson | 17 September 2013, 17:35:09 UTC | work so far! | 23 September 2013, 18:57:47 UTC |
| ed828a5 | Gabriel Sanderson | 16 September 2013, 19:43:07 UTC | First pass top-down work, mostly from Friday. Simplify generate_result. Move all validation to one method. Move all workflow input generation to one method. Use Build clumps. | 23 September 2013, 18:57:47 UTC |
| 47174c2 | APipe Tester | 23 September 2013, 17:07:55 UTC | Updated `gmt` tab completion. | 23 September 2013, 17:07:55 UTC |
| f47736b | APipe Tester | 23 September 2013, 17:07:05 UTC | Updated `genome` tab completion. | 23 September 2013, 17:07:05 UTC |
| ec056ca | APipe Tester | 23 September 2013, 17:05:11 UTC | Updated class browser cache. | 23 September 2013, 17:05:11 UTC |
| 31b088c | Thomas Mooney | 23 September 2013, 15:45:11 UTC | Don't remove models with builds by default. | 23 September 2013, 15:45:11 UTC |
| 9e63476 | apregier | 23 September 2013, 15:42:11 UTC | Merge branch 'annovar' into gb_master | 23 September 2013, 15:42:11 UTC |
| b7e9367 | apregier | 23 September 2013, 15:36:21 UTC | Optionally add rsid to maf file and allow multiple annotations per variant | 23 September 2013, 15:39:03 UTC |
| 7ac61bb | apregier | 23 September 2013, 15:34:37 UTC | Add optional regions to igv multi | 23 September 2013, 15:39:03 UTC |
| d42975a | Thomas Mooney | 23 September 2013, 15:33:54 UTC | Don't present model removal as an option to everyday users. We want to preserve models and builds as a record of past processing. | 23 September 2013, 15:33:54 UTC |
| c59be07 | Nathan Nutter | 23 September 2013, 14:36:52 UTC | use test factory so objects are valid | 23 September 2013, 14:37:26 UTC |
| bcb03d3 | Nathan Nutter | 20 September 2013, 20:04:19 UTC | sort use statements | 23 September 2013, 14:37:26 UTC |
| 04e7021 | Nathan Nutter | 20 September 2013, 20:03:36 UTC | use test factory to create a valid library | 23 September 2013, 14:37:25 UTC |
| bbdb758 | Nathan Nutter | 20 September 2013, 18:32:59 UTC | use test factory to create model subject The previously created test_subject was not a valid object. | 23 September 2013, 14:37:24 UTC |
| 848cb72 | Nathan Nutter | 19 September 2013, 23:25:04 UTC | allow setup_object to be called more than once Since ProcessingProfiles have to be unique setup_object could only be called once (using all defaults). | 23 September 2013, 14:37:23 UTC |
| 3853125 | Nathan Nutter | 19 September 2013, 23:11:09 UTC | set sequencing_platform so instrument data is a valid object | 23 September 2013, 14:37:23 UTC |
| 23c4827 | Thomas Mooney | 23 September 2013, 13:16:41 UTC | We want to unarchive the *archived* symlinks. | 23 September 2013, 13:16:41 UTC |
| 05811ac | Ben Ainscough | 21 September 2013, 01:22:01 UTC | modified test to a build that fits current assumptions TST1 | 21 September 2013, 01:22:01 UTC |
| a155c34 | Anthony Brummett | 20 September 2013, 20:07:26 UTC | Cache the result for symlinked_allocations() to compensate for slow disks | 20 September 2013, 21:34:23 UTC |
| 967be2c | Ben Ainscough | 20 September 2013, 21:30:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 September 2013, 21:30:10 UTC |
| 0f52a9c | Ben Ainscough | 20 September 2013, 21:29:42 UTC | made circos tool semi functional | 20 September 2013, 21:29:42 UTC |
| 4649901 | Anthony Brummett | 20 September 2013, 19:37:07 UTC | Revert 70daf0 and e5f11a e5f11a seems to have been a mistake | 20 September 2013, 19:37:07 UTC |
| 7c920af | APipe Tester | 20 September 2013, 18:15:27 UTC | Updated `gmt` tab completion. | 20 September 2013, 18:15:27 UTC |
| 56cbfb3 | APipe Tester | 20 September 2013, 18:14:26 UTC | Updated `genome` tab completion. | 20 September 2013, 18:14:26 UTC |
| 1797793 | APipe Tester | 20 September 2013, 18:12:04 UTC | Updated class browser cache. | 20 September 2013, 18:12:04 UTC |
| 8c182e8 | Eddie Belter | 20 September 2013, 18:07:26 UTC | Sync: fix incorrectly named taxon create method | 20 September 2013, 18:07:26 UTC |
| 544f871 | Anthony Brummett | 20 September 2013, 15:35:30 UTC | Reset expected output due to UR's Command::V2 change WRT boolean option docs | 20 September 2013, 15:35:30 UTC |
| 81472b3 | APipe Tester | 20 September 2013, 14:34:51 UTC | updated ur submodule to 638499f | 20 September 2013, 14:34:51 UTC |
| 9c21545 | Mark Burnett | 20 September 2013, 13:47:16 UTC | move where validate is called | 20 September 2013, 13:48:03 UTC |
| 702504f | Mark Burnett | 20 September 2013, 13:22:32 UTC | rename Genome::Workflow to Genome::WorkflowBuilder | 20 September 2013, 13:48:02 UTC |
| 592bbd5 | Mark Burnett | 19 September 2013, 20:00:11 UTC | add Operation->execute also fixes some naming issues with left/right from/to | 20 September 2013, 13:48:01 UTC |
| b4511fc | Mark Burnett | 19 September 2013, 18:55:10 UTC | update tests to use subtest | 20 September 2013, 13:48:01 UTC |
| 60933be | Mark Burnett | 19 September 2013, 16:57:43 UTC | add ability to load xml into objects | 20 September 2013, 13:48:00 UTC |
| d5024dc | Mark Burnett | 19 September 2013, 16:36:35 UTC | add message to _validate_mandatory_inputs | 20 September 2013, 13:47:59 UTC |
| 880d119 | Mark Burnett | 19 September 2013, 15:08:11 UTC | add Genome::Workflow abstraction layer | 20 September 2013, 13:47:59 UTC |
| e32b75a | Nathan Nutter | 19 September 2013, 23:06:27 UTC | convert to test factory | 19 September 2013, 23:07:32 UTC |
| 5fed4d9 | Nathan Nutter | 19 September 2013, 21:30:29 UTC | rename variables so it is easier to refactor | 19 September 2013, 23:07:31 UTC |
| 7d14c04 | Nathan Nutter | 19 September 2013, 22:31:38 UTC | move setup_somatic_variation_build | 19 September 2013, 23:07:30 UTC |
| 1a1de55 | Malachi Griffith | 19 September 2013, 22:08:09 UTC | ClinSeq - Add option to update-analysis to allow skipping of archive checks | 19 September 2013, 22:08:09 UTC |
| 5affd08 | apregier | 19 September 2013, 20:30:27 UTC | Increase temp space requirement for merge sx results | 19 September 2013, 20:43:33 UTC |
| 2cf734c | apregier | 19 September 2013, 20:30:01 UTC | Hard trim CHORI ditag reads at 50 bp | 19 September 2013, 20:31:24 UTC |
| 0b07b29 | Nathan Nutter | 19 September 2013, 20:18:16 UTC | add cell_type to sample so it is a valid object | 19 September 2013, 20:19:56 UTC |
