| e71ece8 | APipe Tester | 23 July 2014, 12:15:22 UTC | Updated class browser cache. | 23 July 2014, 12:15:22 UTC |
| debf0fe | Gabriel Sanderson | 18 July 2014, 22:12:46 UTC | CHANGELOG: CCSVCF-snv now accepts a forced_variations_build_id. This param is the ID of a Genome::Model::Build::ImportedVariationsList. If this is provided, these sites will be force-genotyped, regardless of if the model group contained the calls originally. | 22 July 2014, 22:59:00 UTC |
| 3fd3cd1 | apregier | 22 July 2014, 21:54:36 UTC | Merge branch 'copy' into gb_master | 22 July 2014, 21:54:36 UTC |
| 2ae2f27 | apregier | 22 July 2014, 21:52:57 UTC | Don't call db functions outside of subroutines | 22 July 2014, 21:52:57 UTC |
| 3b00b09 | apregier | 22 July 2014, 20:31:28 UTC | Merge branch 'fireteam' into gb_master | 22 July 2014, 20:31:28 UTC |
| 34d0916 | apregier | 22 July 2014, 19:01:51 UTC | Update expected id | 22 July 2014, 20:30:43 UTC |
| 99b238e | apregier | 22 July 2014, 19:01:28 UTC | Update genome-snapshot-deps | 22 July 2014, 20:30:42 UTC |
| 647b715 | apregier | 22 July 2014, 18:58:05 UTC | Add test cases for factory | 22 July 2014, 20:30:41 UTC |
| 598a7c3 | apregier | 22 July 2014, 18:57:12 UTC | Go on to next roi if error is detected | 22 July 2014, 20:30:41 UTC |
| 0cb7568 | apregier | 22 July 2014, 18:56:49 UTC | Fix warning messages | 22 July 2014, 20:30:40 UTC |
| f766cd0 | apregier | 22 July 2014, 18:55:17 UTC | Move build creation into a test helper | 22 July 2014, 20:30:40 UTC |
| cb817cf | Veena Bhonagiri | 22 July 2014, 20:28:53 UTC | Added snap model files for P. wetsremani | 22 July 2014, 20:28:53 UTC |
| 5783d99 | Feiyu Du | 22 July 2014, 19:11:58 UTC | Add interpreter input validation | 22 July 2014, 19:12:57 UTC |
| 3310af3 | Nathaniel Nutter | 22 July 2014, 19:07:52 UTC | fix unimported functions | 22 July 2014, 19:07:52 UTC |
| 6a778ec | apregier | 22 July 2014, 17:14:17 UTC | Merge branch 'fireteam' into gb_master | 22 July 2014, 17:14:17 UTC |
| a04e732 | apregier | 22 July 2014, 15:45:16 UTC | New test cases for modelpair | 22 July 2014, 17:04:00 UTC |
| 2f32fff | apregier | 22 July 2014, 15:42:59 UTC | Get ROI from builds rather than passing it in separately | 22 July 2014, 17:03:59 UTC |
| 0e22413 | apregier | 18 July 2014, 19:09:11 UTC | Add acmg reports to cle plans | 22 July 2014, 17:03:58 UTC |
| 7b6e2db | apregier | 18 July 2014, 16:09:07 UTC | Revert "add available_fields for filters used as interpreters" This reverts commit 3609063156b2daa6deaded534152d3c257036508. | 22 July 2014, 17:03:57 UTC |
| 52c4520 | apregier | 18 July 2014, 15:38:00 UTC | Increase variant reporting memory requirement | 22 July 2014, 17:03:56 UTC |
| bf60063 | apregier | 18 July 2014, 15:37:34 UTC | Run summary stats commands in the wrapper | 22 July 2014, 17:03:54 UTC |
| 3e9e167 | apregier | 18 July 2014, 15:36:43 UTC | Put indels and snvs in separate reports and logs directories | 22 July 2014, 17:03:52 UTC |
| f9c6be8 | apregier | 17 July 2014, 20:01:06 UTC | Put full and simple cle reports in the same plan file | 22 July 2014, 17:03:52 UTC |
| 39c44c6 | apregier | 17 July 2014, 19:59:38 UTC | add available_fields for filters used as interpreters | 22 July 2014, 17:03:51 UTC |
| 3c381ee | apregier | 17 July 2014, 19:59:17 UTC | Fix resource name | 22 July 2014, 17:03:50 UTC |
| d393ee9 | apregier | 17 July 2014, 14:45:58 UTC | Create input vcf with additional sample name | 22 July 2014, 17:03:49 UTC |
| b416361 | apregier | 14 July 2014, 22:09:36 UTC | Use ModelPair object | 22 July 2014, 17:03:48 UTC |
| e83e6c8 | apregier | 14 July 2014, 20:43:00 UTC | Wrapper for Trio reports | 22 July 2014, 17:03:47 UTC |
| bc6bac4 | apregier | 14 July 2014, 20:39:15 UTC | Call correct method to get feature list from reference | 22 July 2014, 17:03:47 UTC |
| 5d32f52 | Jim Weible | 21 July 2014, 19:29:15 UTC | sync additional qc metrics from lims (AUE-269) | 21 July 2014, 19:29:15 UTC |
| 1e7e913 | Susanna Siebert | 21 July 2014, 18:54:46 UTC | Refactor the 'with many sample names' system for variant reporting - Have the interpreters return a field name in the format <sample_name>_<field_name> for interpreters that use many samples and return the same fields for each (in contrast to interpreters that take values of many samples and do calculations on them, e.g. min coverage observed) - Add helper functions for the new format and have the available_fields, headers, and available_fields_dict use those - The header fields in the FullReporter and available fields from its interpreters now match up and can be automatically validated. - Future complex reporters can utilize the new system to also have headers and interpreter available_fields match up. - New module Reporter/WithHeaderAndSampleNames.pm that inherits from Reporter/WithHeader because the available_field_dicts needs to know about the samples - New test reporter and interpreter Framework/Test/WithHeaderAndSampleNamesReporter.pm and Framework/Test/WithManySampleNamesInterpreter.pm that implement the new system - Various test files to test the new functionality | 21 July 2014, 19:11:29 UTC |
| 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 |
