| 80bc127 | APipe Tester | 19 July 2014, 12:16:32 UTC | Updated `genome` tab completion. | 19 July 2014, 12:16:32 UTC |
| dd88d4e | APipe Tester | 19 July 2014, 12:15:10 UTC | Updated class browser cache. | 19 July 2014, 12:15:10 UTC |
| 761dd33 | Ian Ferguson | 18 July 2014, 20:32:36 UTC | Update define docs test for DiffExp | 18 July 2014, 20:32:36 UTC |
| 9d28287 | Ian Ferguson | 18 July 2014, 20:19:54 UTC | Remove old condition strings from DiffExp | 18 July 2014, 20:19:54 UTC |
| 34932d9 | Ian Ferguson | 17 July 2014, 20:07:56 UTC | Update ClinSeq interface to DifferentialExpression | 18 July 2014, 19:45:56 UTC |
| 4e7db70 | Ian Ferguson | 01 May 2014, 22:38:26 UTC | Add 'condition_pairs' to DifferentialExpression Instead of using condition_labels_string and condition_model_ids_string as inputs to DifferentialExpression models, start using an is_many condition_pairs input. Read 'doc' string of the inputs for more details. This commit keeps both the old and new inputs to aid backfilling. | 18 July 2014, 19:45:55 UTC |
| 9651588 | Susanna Siebert | 18 July 2014, 18:26:42 UTC | corrected the calculation of the minimum coverage observed | 18 July 2014, 18:38:45 UTC |
| 3691f8b | apregier | 18 July 2014, 18:38:09 UTC | Merge branch 'updated' into gb_master | 18 July 2014, 18:38:09 UTC |
| 7435e9e | apregier | 18 July 2014, 18:37:14 UTC | Track tumor-only plan file in repo | 18 July 2014, 18:37:14 UTC |
| 9186026 | apregier | 18 July 2014, 17:59:35 UTC | Merge branch 'updated' into gb_master | 18 July 2014, 17:59:35 UTC |
| f1bdfcc | apregier | 18 July 2014, 17:49:42 UTC | Use caf instead of gmaf | 18 July 2014, 17:55:05 UTC |
| 2e186c2 | Susanna Siebert | 18 July 2014, 15:17:50 UTC | the insertion_centric param for bam readcount should be set to 1 for indel reports | 18 July 2014, 15:18:03 UTC |
| bd35a0d | Susanna Siebert | 18 July 2014, 13:55:22 UTC | change variant type interpreter to output ins and del instead of indel | 18 July 2014, 15:18:03 UTC |
| a851baf | Susanna Siebert | 18 July 2014, 13:54:14 UTC | remove breakpoints | 18 July 2014, 15:18:03 UTC |
| 1a02dda | Nathaniel Nutter | 18 July 2014, 00:29:55 UTC | count changes to queue item as modifications All three branches result in a change to a database-sourced object so count all three as a modification. This also addresses the problem that when modify_index failed indefinitely then memory would grow indefinitely. | 18 July 2014, 00:29:55 UTC |
| ad1a87a | Eddie Belter | 17 July 2014, 21:34:18 UTC | RefineReads: stop saving results in a hash | 17 July 2014, 21:37:08 UTC |
| f7161f2 | Eddie Belter | 17 July 2014, 20:46:34 UTC | RefineReads: add gatk base recalibrator and indel realigner | 17 July 2014, 21:37:07 UTC |
| 916c9f9 | Eddie Belter | 17 July 2014, 20:46:03 UTC | RefineReads: add results method for name to gatk base | 17 July 2014, 21:37:06 UTC |
| 511fba1 | Eddie Belter | 17 July 2014, 20:03:29 UTC | RefineRwads: make GATK base command | 17 July 2014, 21:37:06 UTC |
| 14fb7fc | Nathaniel Nutter | 17 July 2014, 21:04:59 UTC | get_or_create needs to catch expcetions from create | 17 July 2014, 21:04:59 UTC |
| 795683e | Nathaniel Nutter | 16 July 2014, 19:20:40 UTC | fix failure in test due to incomplete cleanup on SR failure Previously the test was passing due to a bug in Genome::SoftwareResult's get_or_create that made the exception thrown here never make a second get attempt. Once that was fixed this started failing because the creation cleanup left the object created (by UR::Object) behind. | 17 July 2014, 21:04:30 UTC |
| 8223e08 | Nathaniel Nutter | 16 July 2014, 19:20:10 UTC | can't propogate exception or something swallows it | 17 July 2014, 21:04:28 UTC |
| efc605b | Nathaniel Nutter | 15 July 2014, 23:26:53 UTC | catch create exceptions within get_or_create get_or_create depends on retrying a get after create fails so if create threw an exception then get_or_create would fail even though it didn't necessarily need to. | 17 July 2014, 21:04:27 UTC |
| 418b03f | Nathaniel Nutter | 15 July 2014, 23:06:42 UTC | remove TODO comment I also don't think it's correct anymore since Genome::Sys handles cleanup for locks (as long as Perl isn't Killed). | 17 July 2014, 21:04:26 UTC |
| 9a6ef9e | Nathaniel Nutter | 15 July 2014, 23:06:19 UTC | whitespace | 17 July 2014, 21:04:24 UTC |
| 734c456 | apregier | 17 July 2014, 20:55:23 UTC | Merge branch 'updated' into gb_master | 17 July 2014, 20:55:23 UTC |
| f4474f9 | apregier | 17 July 2014, 20:54:36 UTC | vep terms is no longer a param | 17 July 2014, 20:54:36 UTC |
| 0b4d50d | apregier | 17 July 2014, 20:51:32 UTC | Merge branch 'updated' into gb_master | 17 July 2014, 20:51:32 UTC |
| 42e5f29 | apregier | 10 July 2014, 21:02:55 UTC | Throw exception if VEP fails to execute correctly | 17 July 2014, 20:50:04 UTC |
| 36a22c9 | apregier | 10 July 2014, 21:01:37 UTC | Always use SO terms in VEP expert | 17 July 2014, 20:50:03 UTC |
| d820706 | Jim Weible | 17 July 2014, 16:14:23 UTC | genome processing-profile describe no longer falsely describes values of "0" as "<NULL>" | 17 July 2014, 16:14:36 UTC |
| 9e91dbb | Susanna Siebert | 17 July 2014, 15:19:30 UTC | filters always have the available field "filter_status" | 17 July 2014, 15:19:30 UTC |
| 329c949 | Susanna Siebert | 17 July 2014, 14:47:50 UTC | preliminiary finished version of the full reporter and plan files | 17 July 2014, 14:50:48 UTC |
| 56f2aaa | Susanna Siebert | 17 July 2014, 13:47:28 UTC | remove unneeded columns used for filter validation | 17 July 2014, 14:50:48 UTC |
| 198467d | dmorton | 16 July 2014, 21:23:24 UTC | Stub out symlinking This was accessing the external Amber service, which was unintended. | 16 July 2014, 21:24:51 UTC |
| 5f65831 | dmorton | 16 July 2014, 21:22:17 UTC | Ensure test objects can create valid sql While this does not affect the outcome of the test this will reduce the spam created by the test. | 16 July 2014, 21:24:51 UTC |
| 999c9a6 | Anthony Brummett | 16 July 2014, 19:22:30 UTC | use croak to tell where the rename is called from | 16 July 2014, 19:22:30 UTC |
| d5de69e | apregier | 16 July 2014, 18:25:25 UTC | Merge branch 'copy' into gb_master | 16 July 2014, 18:25:25 UTC |
| 7b2a19a | apregier | 16 July 2014, 18:21:33 UTC | Add new hash entry | 16 July 2014, 18:21:41 UTC |
| 327696c | Susanna Siebert | 16 July 2014, 15:07:23 UTC | test for CAF interpreter | 16 July 2014, 15:07:23 UTC |
| 427dd9e | Susanna Siebert | 16 July 2014, 13:47:09 UTC | subroutine translated_input_names should only work on single properties | 16 July 2014, 13:47:09 UTC |
| 7c0fd56 | Susanna Siebert | 15 July 2014, 20:22:15 UTC | First pass at changes needed to work with is_many translated inputs (doesn't work yet) | 16 July 2014, 13:21:49 UTC |
| 00fe33c | Susanna Siebert | 15 July 2014, 20:19:12 UTC | dbsnp caf interpreter | 16 July 2014, 13:15:22 UTC |
| 657b7a6 | Susanna Siebert | 15 July 2014, 20:18:53 UTC | reporter and plan for CLE full variant report | 16 July 2014, 13:15:22 UTC |
| 35963e8 | Susanna Siebert | 15 July 2014, 20:17:33 UTC | resource provider need dbsnp_vcf to run dbsnp expert | 16 July 2014, 13:15:22 UTC |
| 8742579 | Susanna Siebert | 15 July 2014, 20:16:43 UTC | interpreter to output min coverage value between multiple samples | 16 July 2014, 13:15:22 UTC |
| 21c083b | Susanna Siebert | 15 July 2014, 20:14:29 UTC | interpreter to output the max vaf value between multiple samples | 16 July 2014, 13:15:21 UTC |
| 062de09 | Susanna Siebert | 15 July 2014, 20:13:52 UTC | interpreter to output vaf metrics for multiple samples | 16 July 2014, 13:15:21 UTC |
| 400e0d1 | Susanna Siebert | 15 July 2014, 18:19:04 UTC | Add variant caller count to interpreter output | 16 July 2014, 13:15:21 UTC |
| 99550ed | Susanna Siebert | 15 July 2014, 18:16:14 UTC | refactor for clarity | 16 July 2014, 13:15:21 UTC |
| ac542a9 | dmorton | 16 July 2014, 02:30:14 UTC | Allow Reporters to have translated is_many inputs | 16 July 2014, 02:30:14 UTC |
| 6d55096 | APipe Tester | 15 July 2014, 22:07:26 UTC | updated graphite submodule to b1a942f | 15 July 2014, 22:52:47 UTC |
| 193a0d1 | apregier | 15 July 2014, 22:09:33 UTC | Merge branch 'copy' into gb_master | 15 July 2014, 22:09:33 UTC |
| 2405ad6 | apregier | 15 July 2014, 22:06:08 UTC | Sub underbars for spaces | 15 July 2014, 22:06:08 UTC |
| 6d02645 | apregier | 15 July 2014, 21:44:29 UTC | Merge branch 'copy' into gb_master | 15 July 2014, 21:44:29 UTC |
| 27197f3 | apregier | 15 July 2014, 21:40:33 UTC | Add hash entries for additional capture reagents | 15 July 2014, 21:40:56 UTC |
| 086eede | Gabriel Sanderson | 15 July 2014, 20:03:29 UTC | Merge branch 'master' into gotcloud | 15 July 2014, 20:03:29 UTC |
| 1ed4813 | Nathaniel Nutter | 15 July 2014, 19:40:21 UTC | add CQID status to ConfigForInstrumentData | 15 July 2014, 19:43:00 UTC |
| f5596e7 | Nathaniel Nutter | 15 July 2014, 19:21:20 UTC | fix warning when status is undefined | 15 July 2014, 19:42:59 UTC |
| ac27daf | Nathaniel Nutter | 14 July 2014, 22:02:33 UTC | remove eval | 15 July 2014, 19:42:58 UTC |
| cbe5d88 | Nathaniel Nutter | 14 July 2014, 22:02:04 UTC | deduplicate search queue before processing | 15 July 2014, 19:42:58 UTC |
| 410b4b2 | Nathaniel Nutter | 14 July 2014, 22:01:22 UTC | fix old typo | 15 July 2014, 19:42:56 UTC |
| 06955e1 | Ian Ferguson | 14 July 2014, 18:23:27 UTC | Add bwa-0.7.10 to GMT/Bwa.pm | 14 July 2014, 18:23:27 UTC |
| 1683cfa | Nathaniel Nutter | 14 July 2014, 14:37:18 UTC | add counter intstrumentation for modify_index success and failure | 14 July 2014, 14:38:38 UTC |
| 8f0caf8 | Nathaniel Nutter | 14 July 2014, 14:36:10 UTC | add timer instrumentation around modify_index | 14 July 2014, 14:36:10 UTC |
| 153c366 | Nathaniel Nutter | 14 July 2014, 14:25:51 UTC | set the (forked) process name Set the (forked) process name so we can know what's being worked on and so it's acknowledged that it's a fork and not a duplicate daemon. | 14 July 2014, 14:25:51 UTC |
| d6727b3 | APipe Tester | 12 July 2014, 12:16:40 UTC | Updated `genome` tab completion. | 12 July 2014, 12:16:40 UTC |
| 83ba091 | APipe Tester | 12 July 2014, 12:15:20 UTC | Updated class browser cache. | 12 July 2014, 12:15:20 UTC |
| 875626f | Susanna Siebert | 11 July 2014, 20:16:22 UTC | fixed incorrect test for retrieval of seg dup feature list | 11 July 2014, 20:16:22 UTC |
| 6d8cd33 | Susanna Siebert | 11 July 2014, 19:35:31 UTC | add example resource files for cle testing | 11 July 2014, 19:51:08 UTC |
| 97fe15c | Susanna Siebert | 11 July 2014, 18:10:07 UTC | removed breakpoint | 11 July 2014, 19:51:07 UTC |
| 21207d3 | Susanna Siebert | 11 July 2014, 18:09:09 UTC | fixed bug in the hash creation for unknown readcounts | 11 July 2014, 19:51:07 UTC |
| 90be793 | Susanna Siebert | 11 July 2014, 18:08:39 UTC | fixed typo for segmental duplications | 11 July 2014, 19:51:07 UTC |
| ade4035 | Jason Walker | 11 July 2014, 18:07:50 UTC | initial revision of alignment summary command for Somatic Validation models. | 11 July 2014, 18:07:50 UTC |
| 7c2bf2f | Todd Hepler | 11 July 2014, 16:55:06 UTC | change LSF queue for downloads https://jira.gsc.wustl.edu/browse/LS-1222 | 11 July 2014, 16:55:06 UTC |
| 06399a6 | APipe Tester | 11 July 2014, 12:16:36 UTC | Updated `genome` tab completion. | 11 July 2014, 12:16:36 UTC |
| 8af723d | APipe Tester | 11 July 2014, 12:15:08 UTC | Updated class browser cache. | 11 July 2014, 12:15:08 UTC |
| 1b331eb | apregier | 09 July 2014, 22:00:07 UTC | Use sort -V to order chromosomes appropriately | 10 July 2014, 22:33:40 UTC |
| 700da9f | Gabriel Sanderson | 07 July 2014, 23:13:47 UTC | Added a command to combine snv and indel reports | 10 July 2014, 22:33:40 UTC |
| 92c2872 | dmorton | 10 July 2014, 22:03:41 UTC | Update plan_files for file-based changes | 10 July 2014, 22:03:41 UTC |
| 38451bc | dmorton | 10 July 2014, 22:02:31 UTC | Change HASH to Text (json encoded) Since you cannot shortcut on a HASH type input, we json encode all such inputs (in the input_hash method) and then decode it in the Result object. | 10 July 2014, 22:02:31 UTC |
| 876ab49 | dmorton | 10 July 2014, 22:00:34 UTC | Remove environment-variables from command It turns out that you cannot do it this way. By the time the environment variables are changed they've already been checked. If we want to set these for real we might have to shell out and run another command with these environment variables set. | 10 July 2014, 22:00:34 UTC |
| 6644136 | dmorton | 10 July 2014, 21:07:29 UTC | use Genome::Sys->rsync_directory properly | 10 July 2014, 21:09:39 UTC |
| b9dbb54 | apregier | 10 July 2014, 20:55:57 UTC | Merge branch 'fireteam' into gb_master | 10 July 2014, 20:55:57 UTC |
| 42ced24 | apregier | 10 July 2014, 20:48:11 UTC | Use test components instead of production SimpleReporter components | 10 July 2014, 20:54:28 UTC |
| 0c97c20 | APipe Tester | 10 July 2014, 19:06:45 UTC | updated ur submodule to 759485b | 10 July 2014, 20:47:42 UTC |
| 563cbfd | dmorton | 10 July 2014, 20:25:53 UTC | Ensure that test-data is not on an allocation when tests are run | 10 July 2014, 20:25:53 UTC |
| 6f57c57 | dmorton | 09 July 2014, 19:46:38 UTC | Experts now 'provides_annotations' Filters and Interpreters can now 'requires_annotations'. This allows for combination Experts that provide multiple kinds of annotations. It also allows filters and interpreters to be satisfied by any of a number of potentially compatible experts. | 10 July 2014, 19:00:33 UTC |
| 4ad4892 | dmorton | 09 July 2014, 18:10:36 UTC | Move base reporter into Framework directory | 10 July 2014, 19:00:32 UTC |
| dcdc0b7 | dmorton | 09 July 2014, 04:39:46 UTC | bump version of test data for vep expert We're not ready to allow custom_annotation_tags just yet | 10 July 2014, 19:00:32 UTC |
| b049bb6 | dmorton | 08 July 2014, 21:34:14 UTC | Add new command 'CreateReport' | 10 July 2014, 19:00:32 UTC |
| 895a2e1 | dmorton | 09 July 2014, 03:58:08 UTC | add missing import | 10 July 2014, 19:00:32 UTC |
| 96e67bf | dmorton | 09 July 2014, 03:56:12 UTC | Add Framework/Test These packages will allow us to test without referencing our production experts/interpreters/filters/reporters. | 10 July 2014, 19:00:32 UTC |
| 6f7554b | dmorton | 09 July 2014, 03:54:10 UTC | Add test_expert_is_registered to test_helpers | 10 July 2014, 19:00:32 UTC |
| f310973 | dmorton | 08 July 2014, 20:30:14 UTC | rename annotation_vcf to dbsnp_vcf | 10 July 2014, 19:00:32 UTC |
| 03c6568 | dmorton | 08 July 2014, 20:26:55 UTC | Attempt to lookup allocation before md5sum'ing files | 10 July 2014, 19:00:32 UTC |
| f455953 | dmorton | 07 July 2014, 23:21:25 UTC | Rename test from Plan.t to MasterPlan.t | 10 July 2014, 19:00:31 UTC |
| ed63c61 | dmorton | 07 July 2014, 23:08:02 UTC | Dbsnp expert takes annotation_vcf instead of ImportedVariation build | 10 July 2014, 19:00:31 UTC |
| dc50ef4 | dmorton | 07 July 2014, 21:45:20 UTC | MasterPlan can now validate a ResourceProvider | 10 July 2014, 19:00:31 UTC |
| 18165b9 | dmorton | 07 July 2014, 21:44:32 UTC | Allow ResourceProviders to be read from and written to files (yaml) | 10 July 2014, 19:00:31 UTC |
