| 61b8b89 | apregier | 15 April 2014, 22:00:14 UTC | Merge branch 'updated' into gb_master | 15 April 2014, 22:00:14 UTC |
| cdefba1 | apregier | 15 April 2014, 21:55:37 UTC | Add a new interface to vep command Gets the api and cache through the ensembl version instead of the annotation build | 15 April 2014, 21:58:34 UTC |
| a0fe4a2 | apregier | 15 April 2014, 21:28:56 UTC | Put most functionality into a base class | 15 April 2014, 21:58:32 UTC |
| 5f28ead | apregier | 15 April 2014, 20:15:59 UTC | Move stage method to cache object | 15 April 2014, 21:58:30 UTC |
| e07ab68 | apregier | 15 April 2014, 20:02:49 UTC | whitespace | 15 April 2014, 21:58:29 UTC |
| 6b8a858 | apregier | 15 April 2014, 20:01:46 UTC | Use plugin object | 15 April 2014, 21:58:28 UTC |
| 2191537 | apregier | 15 April 2014, 20:00:20 UTC | Make transient properties Text instead of String This way they don't get slurped in as string properties | 15 April 2014, 21:58:28 UTC |
| 34593fb | apregier | 15 April 2014, 19:59:37 UTC | Add vep plugin object | 15 April 2014, 21:58:27 UTC |
| 83654b1 | apregier | 15 April 2014, 18:21:32 UTC | Separate staging plugin config from querying for plugin args | 15 April 2014, 21:58:25 UTC |
| 84b411e | apregier | 15 April 2014, 17:23:51 UTC | Create one plugin arg string at a time | 15 April 2014, 21:58:24 UTC |
| 1a8d4b3 | apregier | 15 April 2014, 17:06:20 UTC | Extract method to get or create the temp dir | 15 April 2014, 21:58:23 UTC |
| 29ffa4e | apregier | 15 April 2014, 15:39:00 UTC | Extract methods to construct and run the command | 15 April 2014, 21:58:23 UTC |
| 3f6f5ed | apregier | 15 April 2014, 15:29:31 UTC | Extract method for db_connect params | 15 April 2014, 21:58:22 UTC |
| 2931e87 | apregier | 15 April 2014, 15:25:04 UTC | Extract methods for plugin_args and cache_args | 15 April 2014, 21:58:21 UTC |
| 7227ceb | apregier | 15 April 2014, 14:56:27 UTC | Extract custom_args method | 15 April 2014, 21:58:21 UTC |
| 01d4112 | apregier | 15 April 2014, 14:52:41 UTC | Make accessor functions rather than local variables | 15 April 2014, 21:58:20 UTC |
| f60c49c | apregier | 15 April 2014, 14:50:17 UTC | Move string args tweaking into subroutine | 15 April 2014, 21:58:19 UTC |
| ff9b930 | APipe Tester | 15 April 2014, 20:46:24 UTC | updated jenkins submodule to c81b2ba | 15 April 2014, 20:46:24 UTC |
| c379d02 | APipe Tester | 15 April 2014, 20:34:26 UTC | updated jenkins submodule to 8363e5f | 15 April 2014, 20:34:26 UTC |
| e26c217 | Thomas Mooney | 15 April 2014, 20:19:13 UTC | Do all the sorting and filtering logic even if from an Analysis Project This change is pursuant to RT#98634. | 15 April 2014, 20:19:13 UTC |
| c69f825 | APipe Tester | 15 April 2014, 20:04:30 UTC | updated jenkins submodule to b9e8e79 | 15 April 2014, 20:04:30 UTC |
| 6ffd932 | APipe Tester | 15 April 2014, 19:55:31 UTC | updated jenkins submodule to 8c8edaa | 15 April 2014, 19:55:31 UTC |
| b2f914b | APipe Tester | 15 April 2014, 19:52:34 UTC | updated jenkins submodule to ffac64e | 15 April 2014, 19:52:34 UTC |
| 16f6353 | APipe Tester | 15 April 2014, 19:46:53 UTC | updated jenkins submodule to ad170e0 | 15 April 2014, 19:46:53 UTC |
| 3f27b04 | Thomas Mooney | 15 April 2014, 14:20:33 UTC | Update test to have less trailing whitespace. | 15 April 2014, 14:20:33 UTC |
| 081bd70 | Thomas Mooney | 15 April 2014, 14:08:51 UTC | Remove trailing whitespace. | 15 April 2014, 14:08:51 UTC |
| ee2b3ac | apregier | 15 April 2014, 14:08:16 UTC | Merge branch 'updated' into gb_master | 15 April 2014, 14:08:16 UTC |
| a6bea93 | apregier | 14 April 2014, 22:45:03 UTC | Extract method to resolve format and input file | 15 April 2014, 14:05:27 UTC |
| 48d4f56 | apregier | 14 April 2014, 22:07:51 UTC | Extract script_path method | 15 April 2014, 14:05:27 UTC |
| cbc8974 | apregier | 14 April 2014, 22:05:26 UTC | Extract annotation_build method | 15 April 2014, 14:05:25 UTC |
| 9ba5b60 | APipe Tester | 15 April 2014, 12:18:59 UTC | Updated `gmt` tab completion. | 15 April 2014, 12:18:59 UTC |
| 0c5afc2 | APipe Tester | 15 April 2014, 12:18:14 UTC | Updated `genome` tab completion. | 15 April 2014, 12:18:14 UTC |
| 0caaa3b | APipe Tester | 15 April 2014, 12:16:34 UTC | Updated class browser cache. | 15 April 2014, 12:16:34 UTC |
| d0ec257 | Gabriel Sanderson | 15 April 2014, 00:20:18 UTC | minor param cleanup | 15 April 2014, 00:20:18 UTC |
| a29e56a | Gabriel Sanderson | 15 April 2014, 00:14:57 UTC | Refactored code out of adaptor tests into an adaptor testhelper -- still could use a little cleanup with lots of parameters passing around | 15 April 2014, 00:14:57 UTC |
| 0981ab9 | Gabriel Sanderson | 14 April 2014, 22:22:22 UTC | Added SomaticValidation adaptor and test | 14 April 2014, 22:22:22 UTC |
| a16c4e2 | Gabriel Sanderson | 14 April 2014, 21:54:19 UTC | Move resolve_annotation_build up to the base class | 14 April 2014, 21:54:19 UTC |
| 95bfc68 | Feiyu Du | 14 April 2014, 21:35:35 UTC | Add JoinxVcfAnnoate command, result and test | 14 April 2014, 21:35:35 UTC |
| 975be0d | Nathaniel Nutter | 14 April 2014, 21:24:21 UTC | refactor Genome::Sys::Lock (prep for Nessy) | 14 April 2014, 21:24:21 UTC |
| 7f9f64f | Nathaniel Nutter | 11 April 2014, 19:34:50 UTC | activate nessy code while testing | 14 April 2014, 21:24:11 UTC |
| 667d887 | Nathaniel Nutter | 11 April 2014, 00:44:07 UTC | add wait_announce_internal to quiet tests | 14 April 2014, 21:24:10 UTC |
| e45a7dd | Nathaniel Nutter | 11 April 2014, 00:33:53 UTC | set max_try and block_sleep to quicken test | 14 April 2014, 21:24:09 UTC |
| ff29aad | Nathaniel Nutter | 10 April 2014, 22:53:31 UTC | should only be unlocking file lock | 14 April 2014, 21:24:09 UTC |
| 553a68e | Nathaniel Nutter | 10 April 2014, 22:25:13 UTC | put a more reasonable cap on retries | 14 April 2014, 21:24:08 UTC |
| 29c58f4 | Nathaniel Nutter | 10 April 2014, 22:10:10 UTC | limit interface to function that implements the behaviour These two tests were testing behaviour that was specific to the file based implementation. | 14 April 2014, 21:24:07 UTC |
| c96dfe3 | Nathaniel Nutter | 10 April 2014, 22:09:23 UTC | abstract lock/unlock code to reuse for special cases | 14 April 2014, 21:24:07 UTC |
| 0ad9746 | Nathaniel Nutter | 10 April 2014, 22:08:59 UTC | add basic input validation | 14 April 2014, 21:24:06 UTC |
| acd7423 | Nathaniel Nutter | 14 April 2014, 14:37:49 UTC | remove duplicated test condition | 14 April 2014, 21:24:05 UTC |
| 23938e6 | Nathaniel Nutter | 10 April 2014, 21:42:11 UTC | clear_state in child processes | 14 April 2014, 21:24:05 UTC |
| 2539dd2 | Nathaniel Nutter | 10 April 2014, 21:37:11 UTC | use fork_lock_resource instead of locally overriding state | 14 April 2014, 21:24:04 UTC |
| 3b34153 | Nathaniel Nutter | 10 April 2014, 21:24:55 UTC | add clear_start method to get clean child processes | 14 April 2014, 21:24:03 UTC |
| 406f61d | Nathaniel Nutter | 11 April 2014, 20:59:53 UTC | add periodic announcement while waiting on lock | 14 April 2014, 21:24:03 UTC |
| b5f5617 | Nathaniel Nutter | 14 April 2014, 14:03:01 UTC | set a minimum timeout | 14 April 2014, 21:24:02 UTC |
| f8561f3 | Nathaniel Nutter | 11 April 2014, 20:56:49 UTC | move wait_announce_interval default up to lock_resource | 14 April 2014, 21:24:01 UTC |
| 7a8d5d0 | Gabriel Sanderson | 14 April 2014, 21:18:05 UTC | Rely on output_file_path instead of get_vcf | 14 April 2014, 21:18:15 UTC |
| c522ddb | Adam Coffman | 14 April 2014, 21:08:22 UTC | is_concrete is now a public method | 14 April 2014, 21:08:22 UTC |
| 0245fc2 | Gabriel Sanderson | 14 April 2014, 20:49:28 UTC | Fixed typo in software_result class | 14 April 2014, 20:49:28 UTC |
| 8a68633 | dmorton | 14 April 2014, 18:57:28 UTC | Don't crash build when vcf sample name is different from aligned-reads This happens for example in samples from TCGA because of some logic here: Genome/Model/Tools/Vcf/Convert/Base.pm | 14 April 2014, 18:57:28 UTC |
| a9c1137 | dmorton | 14 April 2014, 16:14:45 UTC | Annotation::Vep classes inherit from Annotation::Detail base classes | 14 April 2014, 16:14:45 UTC |
| c92a10e | dmorton | 14 April 2014, 16:13:00 UTC | Name class correctly and remove unused params before passing on | 14 April 2014, 16:13:00 UTC |
| ed814f9 | dmorton | 14 April 2014, 16:09:15 UTC | Factor out test_cmd_and_result_are_in_sync to TestHelpers | 14 April 2014, 16:09:15 UTC |
| 16498e5 | dmorton | 14 April 2014, 03:09:19 UTC | Add Command and Result to add readcount info to a vcf_result | 14 April 2014, 15:27:33 UTC |
| 64e7621 | dmorton | 14 April 2014, 03:05:54 UTC | Change inputs to AnnotateWithReadcounts We cannot rely on UR to keep is_many properties in any particular order, so we have to combine these two fields. While we're at it, since sample_names aren't in fact useful except to get at the column index in the vcf-header, lets go ahead and just require the index. | 14 April 2014, 15:27:33 UTC |
| 7ce1aa5 | dmorton | 14 April 2014, 03:02:07 UTC | Fix up how to get param_names and input_names In particular, we have to be careful with params on software results. | 14 April 2014, 15:27:32 UTC |
| 77092ef | dmorton | 14 April 2014, 02:54:38 UTC | File::Vcf::Writer can write bgzipped files | 14 April 2014, 15:27:32 UTC |
| f933d61 | dmorton | 11 April 2014, 21:06:07 UTC | Add sample_name accessor for Readcount::Result | 14 April 2014, 15:27:32 UTC |
| e43910c | dmorton | 11 April 2014, 21:04:50 UTC | Make base classes for Annotation commands and results | 14 April 2014, 15:27:32 UTC |
| abc22f5 | dmorton | 11 April 2014, 20:09:36 UTC | Moved command into gmt | 14 April 2014, 15:27:32 UTC |
| bdb8d0b | Eddie Belter | 11 April 2014, 21:33:47 UTC | ClinSeq: rm redirect to dev/null for illumina_info command to investigate failure | 11 April 2014, 21:35:50 UTC |
| f59afd4 | APipe Tester | 11 April 2014, 21:33:00 UTC | updated jenkins submodule to 20afc03 | 11 April 2014, 21:33:00 UTC |
| b9f5fdd | Gabriel Sanderson | 11 April 2014, 20:31:08 UTC | Added Genome::Annotation::Vep and accompanying result and tests. | 11 April 2014, 20:38:38 UTC |
| b228d96 | Gabriel Sanderson | 11 April 2014, 19:17:26 UTC | Add get_tabix_and_gzipped_bed_file to Genome::Featurelist. This will be used for VEP annotation. | 11 April 2014, 20:38:37 UTC |
| 67fb1b3 | Gabriel Sanderson | 11 April 2014, 19:16:33 UTC | Added gzip_file to Genome::Sys, which compresses a file to a target path. | 11 April 2014, 20:38:37 UTC |
| a0e4f64 | Gabriel Sanderson | 09 April 2014, 20:10:27 UTC | added vcf.gz test | 11 April 2014, 20:37:03 UTC |
| fe24c91 | Gabriel Sanderson | 09 April 2014, 19:52:30 UTC | Added VCF test. Updated test directories. | 11 April 2014, 20:36:48 UTC |
| 4f26a83 | apregier | 11 April 2014, 19:01:08 UTC | Merge branch 'updated' into gb_master | 11 April 2014, 19:01:08 UTC |
| ccbb5b4 | David Morton | 11 April 2014, 17:45:30 UTC | Improve tests for Adaptor::SomaticVariation | 11 April 2014, 18:36:52 UTC |
| 6090d88 | David Morton | 11 April 2014, 17:43:16 UTC | Add abstract methods to abstract class Adaptor | 11 April 2014, 18:36:51 UTC |
| 6c7aaf4 | David Morton | 11 April 2014, 17:42:36 UTC | Remove unneeded temp variable $results | 11 April 2014, 18:36:50 UTC |
| 75f7c47 | apregier | 10 April 2014, 21:28:41 UTC | Command to add readcount to vcf sample fields We assume that all readcount files are sorted in the same order as the vcf file, and that they contain only variants in the vcf file. | 11 April 2014, 18:36:50 UTC |
| 0c82324 | apregier | 10 April 2014, 20:19:22 UTC | Get original string from bam-readcount entry | 11 April 2014, 18:36:49 UTC |
| 7b2e71b | apregier | 10 April 2014, 20:15:40 UTC | Catch exceptions if vcf results don't exist There may be builds without vcf results, so we can catch those exceptions and simply return undef. | 11 April 2014, 18:36:49 UTC |
| c761754 | apregier | 10 April 2014, 20:14:08 UTC | Throw exception if files don't exist | 11 April 2014, 18:36:48 UTC |
| d405b9b | apregier | 09 April 2014, 21:45:09 UTC | Catch exceptions if vcf result is not available | 11 April 2014, 18:36:47 UTC |
| bd7a3be | Adam Coffman | 11 April 2014, 17:19:02 UTC | adjust UR constraint to match DB constraint | 11 April 2014, 17:19:02 UTC |
| 5d511c0 | Adam Coffman | 11 April 2014, 17:15:06 UTC | migration to widen name column | 11 April 2014, 17:15:06 UTC |
| 016d2e7 | Adam Coffman | 11 April 2014, 15:21:29 UTC | change subject->sample for somval importer | 11 April 2014, 15:21:29 UTC |
| 702ed35 | APipe Tester | 11 April 2014, 12:18:38 UTC | Updated `gmt` tab completion. | 11 April 2014, 12:18:38 UTC |
| da0e271 | APipe Tester | 11 April 2014, 12:17:54 UTC | Updated `genome` tab completion. | 11 April 2014, 12:17:54 UTC |
| c045cf0 | APipe Tester | 11 April 2014, 12:16:21 UTC | Updated class browser cache. | 11 April 2014, 12:16:21 UTC |
| 10d3651 | Nathaniel Nutter | 11 April 2014, 02:15:38 UTC | Revert "switch _new_style_lock to retry" This reverts commit eccbdeaf713350c4f7c80b70626a62e34ad794c2. | 11 April 2014, 02:15:50 UTC |
| fb00a65 | Chris Miller | 10 April 2014, 23:20:38 UTC | adding option to dump mean and median coverage to a file | 10 April 2014, 23:20:45 UTC |
| 28b1ab0 | Eddie Belter | 10 April 2014, 22:41:30 UTC | Sync/GM: do not die if reallocate fails | 10 April 2014, 22:41:51 UTC |
| 00bf30d | Chris Miller | 10 April 2014, 20:18:00 UTC | correctly match up coordinates from assembly validation | 10 April 2014, 20:18:00 UTC |
| 1104d8d | Chris Miller | 10 April 2014, 19:50:25 UTC | report VAF percentages (50) instead of fractions (0.50) for large indels pulled from assembly validation | 10 April 2014, 19:51:06 UTC |
| eccbdea | Nathaniel Nutter | 10 April 2014, 00:36:34 UTC | switch _new_style_lock to retry In order to provide periodic status updates while waiting on locks like the NFS backend did switch _new_style_lock's timeout to block_sleep and retry max_try times instead of doing one block_sleep * max_try attempt. | 10 April 2014, 19:26:17 UTC |
| 7567de7 | Nathaniel Nutter | 09 April 2014, 22:34:49 UTC | move defaults up so they get passed to both backends | 10 April 2014, 19:26:16 UTC |
| 569f0fa | dmorton | 10 April 2014, 15:45:08 UTC | Don't die when variants-directory isn't found. This behavior is relied on in numerous places in ReferenceAlignment builds. In SomaticVariation and SomaticValidation, I didn't see any eval statements preceeding the calls to ->variants_directory so I think it is safe to relax this check. | 10 April 2014, 15:48:57 UTC |
| c684828 | Susanna Siebert | 10 April 2014, 13:12:12 UTC | Merge branch 'clip_overlap' | 10 April 2014, 13:12:12 UTC |
| f539988 | Susanna Siebert | 10 April 2014, 13:10:14 UTC | implement shortcut method for RefineReads | 10 April 2014, 13:10:14 UTC |
