| cfacb40 | apregier | 28 July 2014, 22:04:19 UTC | Compare output directories in wrapper test | 29 July 2014, 17:24:12 UTC |
| 9b2b5b3 | apregier | 28 July 2014, 22:03:57 UTC | Skip log directories during file comparisons | 29 July 2014, 16:57:27 UTC |
| c90fdc5 | apregier | 28 July 2014, 21:25:39 UTC | Move compare_directories into test helper | 29 July 2014, 16:57:27 UTC |
| f10c48a | apregier | 28 July 2014, 21:21:09 UTC | Add test for running reports starting with wrapper | 29 July 2014, 16:57:26 UTC |
| 0ff30e6 | apregier | 28 July 2014, 21:19:45 UTC | Move build creation to test helper | 29 July 2014, 16:57:25 UTC |
| 11ef056 | apregier | 28 July 2014, 19:28:50 UTC | Change to debug message | 29 July 2014, 16:57:25 UTC |
| fabceec | Thomas Mooney | 29 July 2014, 14:26:50 UTC | Also return if genome_length came back 0 to avoid dividing by it. | 29 July 2014, 14:26:50 UTC |
| d39e1bc | Thomas Mooney | 28 July 2014, 22:34:55 UTC | Remove import of "mode" subroutine from modules no longer using it. | 28 July 2014, 22:34:55 UTC |
| 8b4576d | Avinash Ramu | 28 July 2014, 21:57:01 UTC | revert until test-factory issue is resolved | 28 July 2014, 21:57:01 UTC |
| 6454408 | Malachi Griffith | 28 July 2014, 21:17:33 UTC | update clin-seq default to latest version of cosmic annotation db that has the latest annotations from Ensembl | 28 July 2014, 21:17:33 UTC |
| 8e5da35 | apregier | 28 July 2014, 19:25:45 UTC | Merge branch 'fireteam' into gb_master | 28 July 2014, 19:25:45 UTC |
| 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 |
