| a230115 | apregier | 28 July 2014, 19:05:41 UTC | Revert "catch create exceptions within get_or_create" This reverts commit efc605b1f6a821b3f737ded8fe43e9ff3df7aa2d. | 28 July 2014, 19:06:18 UTC |
| dc594d8 | apregier | 28 July 2014, 19:04:42 UTC | Revert "can't propogate exception or something swallows it" This reverts commit 8223e0899bae5d572647e16c71d7f703f66bd2fc. | 28 July 2014, 19:06:18 UTC |
| 5c3fcb4 | Nathaniel Nutter | 28 July 2014, 18:04:32 UTC | fix issues for RT/100194 - only generate IGV XML files for known references - get tier bed path from Tier result | 28 July 2014, 18:04:32 UTC |
| 1552189 | Nathaniel Nutter | 25 July 2014, 21:19:12 UTC | only generate IGV XML files for known references | 28 July 2014, 17:49:37 UTC |
| 76eaccb | Nathaniel Nutter | 23 July 2014, 22:43:29 UTC | get tier bed path from Tier result | 28 July 2014, 17:49:36 UTC |
| cf8d1a8 | Nathaniel Nutter | 23 July 2014, 22:41:44 UTC | add option to filter results from glob on pattern Maintains support for glob pattern but allows flexibility when needed. | 28 July 2014, 17:49:34 UTC |
| 51cf314 | Nathaniel Nutter | 23 July 2014, 22:40:24 UTC | croak instead of die It's a non-unique pattern which caused the failure so die from caller's perspective (croak). | 28 July 2014, 17:49:32 UTC |
| 9721a52 | APipe Tester | 25 July 2014, 22:35:43 UTC | updated ur submodule to 148d9a2 | 25 July 2014, 22:35:43 UTC |
| 162f89d | Gabriel Sanderson | 25 July 2014, 21:06:38 UTC | Respect GENOME_SOFTWARE_RESULT_TEST_NAME | 25 July 2014, 21:06:45 UTC |
| fc524a7 | Tiandao Li | 25 July 2014, 19:48:12 UTC | model IDs | 25 July 2014, 19:48:12 UTC |
| 82bc726 | Eddie Belter | 25 July 2014, 18:37:51 UTC | InstData Import: basic uses work flow helpers | 25 July 2014, 18:37:51 UTC |
| ec9c7f2 | Eddie Belter | 25 July 2014, 18:15:23 UTC | GMT GeneTorrent: calculate rate limit from lsf rusage | 25 July 2014, 18:15:23 UTC |
| a8b355f | Eddie Belter | 25 July 2014, 16:54:21 UTC | Helpers: add workflow building | 25 July 2014, 16:54:21 UTC |
| 842432a | dmorton | 25 July 2014, 03:03:55 UTC | Don't memoize something that is only called once | 25 July 2014, 03:04:44 UTC |
| 0e44296 | dmorton | 25 July 2014, 03:03:39 UTC | Use differ instead of compare_ok | 25 July 2014, 03:04:43 UTC |
| c1ae14c | dmorton | 25 July 2014, 03:03:00 UTC | Avoid is_many lookups (they're very slow) | 25 July 2014, 03:04:43 UTC |
| cb56939 | dmorton | 25 July 2014, 03:02:35 UTC | Make decode and encode even faster | 25 July 2014, 03:04:43 UTC |
| 7aad445 | dmorton | 25 July 2014, 01:15:10 UTC | Change way that BamReadcount::Entry en(de)codes for vcf | 25 July 2014, 03:04:43 UTC |
| ba26fb7 | dmorton | 24 July 2014, 20:49:50 UTC | use get_class instead of _load | 25 July 2014, 03:04:43 UTC |
| ffc430e | dmorton | 24 July 2014, 20:49:33 UTC | Make factory a package global in plan base class | 25 July 2014, 03:04:43 UTC |
| 75fd898 | dmorton | 24 July 2014, 20:49:00 UTC | stop calling _load more than once | 25 July 2014, 03:04:43 UTC |
| f351889 | dmorton | 24 July 2014, 20:48:13 UTC | Do not report on or try to interpret when all alts are failed | 25 July 2014, 03:04:43 UTC |
| 79bf15d | apregier | 24 July 2014, 21:26:48 UTC | Always print the vcf being used for the report | 24 July 2014, 21:27:28 UTC |
| 599d819 | Tiandao Li | 24 July 2014, 20:07:41 UTC | Concordance using model IDs | 24 July 2014, 20:07:41 UTC |
| 63c17fc | Tiandao Li | 24 July 2014, 20:07:04 UTC | Concordance using model IDs | 24 July 2014, 20:07:04 UTC |
| 75392db | APipe Tester | 24 July 2014, 16:31:11 UTC | updated ur submodule to 990eb36 | 24 July 2014, 16:31:11 UTC |
| fd3d60d | APipe Tester | 24 July 2014, 12:16:36 UTC | Updated `genome` tab completion. | 24 July 2014, 12:16:36 UTC |
| 39c7711 | Gabriel Sanderson | 23 July 2014, 22:11:40 UTC | Updated test output - 1.7 should use zcat and 1.8 should not | 23 July 2014, 22:11:40 UTC |
| 68f42f5 | Gabriel Sanderson | 23 July 2014, 21:51:06 UTC | Only use zcat when required. Joinx 1.8 handles it natively. | 23 July 2014, 21:51:52 UTC |
| db32c9a | Eddie Belter | 23 July 2014, 21:26:16 UTC | InstData: reimport file generator excludes read count and length | 23 July 2014, 21:48:09 UTC |
| b9614ea | Eddie Belter | 23 July 2014, 21:26:16 UTC | InstData: reimport file generator excludes read count and length | 23 July 2014, 21:26:16 UTC |
| 627dbec | Feiyu Du | 23 July 2014, 20:36:36 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 23 July 2014, 20:36:36 UTC |
| 56705f8 | Feiyu Du | 23 July 2014, 20:36:14 UTC | bug fix: reinstall_sub is global | 23 July 2014, 20:36:14 UTC |
| f6e8fc6 | Nathaniel Nutter | 23 July 2014, 19:44:46 UTC | include path in "can't open file" error message | 23 July 2014, 19:44:46 UTC |
| 8bd4866 | Steve Wilkerson | 23 July 2014, 18:30:49 UTC | Changed Differ.t to allow for tests to run from any directory | 23 July 2014, 18:41:09 UTC |
| 388ada2 | Steve Wilkerson | 23 July 2014, 18:13:22 UTC | Ensured use of File::Vcf::Differ was correct | 23 July 2014, 18:41:09 UTC |
| d4e0ab0 | Steve Wilkerson | 23 July 2014, 17:42:58 UTC | Changed HeaderDiff to include to_string subroutine | 23 July 2014, 18:41:08 UTC |
| 9ea8e05 | Steve Wilkerson | 23 July 2014, 17:41:57 UTC | Added POD documentation for Differ, HeaderDiff | 23 July 2014, 18:41:08 UTC |
| 22d199d | Steve Wilkerson | 23 July 2014, 17:39:56 UTC | Added EntryDiff.pm as well as associated tests | 23 July 2014, 18:41:08 UTC |
| b71d543 | Steve Wilkerson | 22 July 2014, 16:00:11 UTC | Added to_hashref to Vcf Entry Object | 23 July 2014, 18:41:08 UTC |
| 26b4635 | Steve Wilkerson | 22 July 2014, 15:42:31 UTC | Extracted all_columns method | 23 July 2014, 18:41:07 UTC |
| 3929f1c | Steve Wilkerson | 22 July 2014, 15:28:08 UTC | Implemented the HeaderDiff's print method and test Implemented the print method in such a way to be more descriptive in explaining differences between vcf file headers. | 23 July 2014, 18:41:07 UTC |
| 2ed2c55 | Steve Wilkerson | 07 July 2014, 14:18:52 UTC | Initial changes with Dave:q | 23 July 2014, 18:41:07 UTC |
| ebc46f2 | apregier | 23 July 2014, 18:32:16 UTC | Merge branch 'fireteam' into gb_master | 23 July 2014, 18:32:16 UTC |
| 7040933 | apregier | 23 July 2014, 18:30:55 UTC | Unique name needs to be truncated in get_class as well | 23 July 2014, 18:30:55 UTC |
| ba5e4ad | apregier | 23 July 2014, 18:15:36 UTC | Merge branch 'fireteam' into gb_master | 23 July 2014, 18:15:36 UTC |
| 8c777a1 | apregier | 23 July 2014, 17:53:14 UTC | Use correct roi accessor for somatic validation | 23 July 2014, 18:09:57 UTC |
| 4df7df1 | apregier | 23 July 2014, 17:52:23 UTC | Fix useless use of string in void context warning | 23 July 2014, 18:09:56 UTC |
| bd197c5 | apregier | 23 July 2014, 17:28:56 UTC | Use unique names for reporters | 23 July 2014, 18:09:55 UTC |
| fff8f47 | apregier | 23 July 2014, 17:16:36 UTC | Allow object names to contain uniquifying information after a 'dot' | 23 July 2014, 18:09:53 UTC |
| 739ad80 | apregier | 23 July 2014, 16:59:01 UTC | Fix output directory name | 23 July 2014, 18:09:51 UTC |
| 9f2de8d | apregier | 23 July 2014, 16:56:55 UTC | Run summary stats first | 23 July 2014, 18:09:50 UTC |
| 8a4552d | apregier | 23 July 2014, 16:55:41 UTC | Hard-code plan files | 23 July 2014, 18:09:49 UTC |
| 3aec9ba | apregier | 23 July 2014, 16:41:37 UTC | Combine snv and indel reports | 23 July 2014, 18:09:48 UTC |
| a603f67 | Feiyu Du | 23 July 2014, 18:02:45 UTC | bug fix | 23 July 2014, 18:02:45 UTC |
| b2ac8f1 | Feiyu Du | 23 July 2014, 17:41:56 UTC | Add unit test to test interpreter input allele validation | 23 July 2014, 17:41:56 UTC |
| 7951868 | Feiyu Du | 23 July 2014, 16:25:00 UTC | add abstract method _interpret_entry to interpreter base class | 23 July 2014, 16:25:00 UTC |
| 9ccbd18 | Feiyu Du | 23 July 2014, 15:51:14 UTC | 1.use Sst::Scalar to handle array comparison 2. rename process_interpret_entry to _interpret_entry for all interpreter subclass | 23 July 2014, 15:51:14 UTC |
| acfc926 | Michael J. Kiwala | 23 July 2014, 15:16:28 UTC | When testing, set the GENOME_TESTING env var | 23 July 2014, 15:16:28 UTC |
| 3a5f7e2 | Michael J. Kiwala | 23 July 2014, 15:06:18 UTC | During testing, cufflinks should request less memory | 23 July 2014, 15:07:19 UTC |
| cfe2afd | Michael J. Kiwala | 23 July 2014, 15:05:16 UTC | New environment variable which should be set during testing | 23 July 2014, 15:05:16 UTC |
| 74310fa | APipe Tester | 23 July 2014, 12:17:24 UTC | Updated `gmt` tab completion. | 23 July 2014, 12:17:24 UTC |
| 651a3a9 | APipe Tester | 23 July 2014, 12:16:45 UTC | Updated `genome` tab completion. | 23 July 2014, 12:16:45 UTC |
| 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 |
