| 73e27ca | Avinash Ramu | 23 May 2014, 13:31:53 UTC | update clin-seq blessed - bamqc | 23 May 2014, 13:31:53 UTC |
| f069aed | APipe Tester | 23 May 2014, 12:19:20 UTC | Updated `genome` tab completion. | 23 May 2014, 12:19:20 UTC |
| 634c351 | APipe Tester | 23 May 2014, 12:17:39 UTC | Updated class browser cache. | 23 May 2014, 12:17:39 UTC |
| 4755788 | Nathaniel Nutter | 22 May 2014, 22:15:54 UTC | add basic test and fixes revealed by test | 22 May 2014, 23:38:08 UTC |
| 7ddb771 | Nathaniel Nutter | 22 May 2014, 21:00:25 UTC | first draft, add command to list build queue for use by cron | 22 May 2014, 23:38:06 UTC |
| 5925c58 | Nathaniel Nutter | 22 May 2014, 18:17:45 UTC | move should_run_as to the model | 22 May 2014, 23:37:05 UTC |
| 8b9d879 | Nathaniel Nutter | 22 May 2014, 17:55:23 UTC | export instrumentation functions | 22 May 2014, 22:19:41 UTC |
| 9b4f321 | Nathaniel Nutter | 22 May 2014, 17:54:58 UTC | export pluck_column_from_class | 22 May 2014, 22:19:40 UTC |
| 24629c5 | Feiyu Du | 22 May 2014, 22:07:09 UTC | fix a command bug | 22 May 2014, 22:07:09 UTC |
| 5befa40 | apregier | 22 May 2014, 20:57:41 UTC | Merge branch 'updated' into gb_master | 22 May 2014, 20:57:41 UTC |
| 7339f93 | apregier | 22 May 2014, 20:53:23 UTC | Max af filter | 22 May 2014, 20:56:29 UTC |
| 571e169 | Ian Ferguson | 22 May 2014, 20:42:30 UTC | Turn off fixmate for Bwamem This adds a method 'requires_fixmate' in AlignmentResult.pm to control running fixmate after alignment. Aligner submodules can disable fixmate by overriding the method 'requires_fixmate' and returning 0. An old check for disabling fixmate for Rtg aligners in AlignmentResult.pm has been removed, and the Rtg aligner modules now override the requires_fixmate method. Bwamem also overrides the method, since fixmate is incompatible with the 0x800 supplementary alignment flag that Bwamem uses. | 22 May 2014, 20:48:17 UTC |
| a241050 | Thomas Mooney | 22 May 2014, 20:31:53 UTC | Reload to get any updates to output_dir from unarchiving. | 22 May 2014, 20:31:53 UTC |
| 631bffc | Susanna Siebert | 22 May 2014, 20:30:20 UTC | Merge branch 'rna_seq' changing MinVafFilter to work with min and max cutoff values | 22 May 2014, 20:30:20 UTC |
| e1db3c6 | Susanna Siebert | 22 May 2014, 20:29:54 UTC | rename filter to vaf-cutoff to make it unique | 22 May 2014, 20:29:54 UTC |
| 24649f2 | Ian Ferguson | 22 May 2014, 20:14:15 UTC | Update Picard version sorting for Picard-1.113 | 22 May 2014, 20:14:15 UTC |
| c785da7 | Susanna Siebert | 22 May 2014, 20:06:43 UTC | add fail test for max vaf | 22 May 2014, 20:06:43 UTC |
| 911bc30 | Susanna Siebert | 22 May 2014, 20:04:25 UTC | added check and test to ensure that max_vaf is larger than min_vaf | 22 May 2014, 20:04:25 UTC |
| 9b81b39 | Susanna Siebert | 22 May 2014, 19:46:49 UTC | add pass tests for max vaf | 22 May 2014, 19:46:49 UTC |
| 46c1687 | Susanna Siebert | 22 May 2014, 19:43:50 UTC | fix the error checking and add test | 22 May 2014, 19:43:50 UTC |
| cf42fa9 | Susanna Siebert | 22 May 2014, 19:33:59 UTC | change MinVafFilter to VafFilter and allow max_value as well as min_value | 22 May 2014, 19:33:59 UTC |
| 92745f6 | apregier | 22 May 2014, 18:56:40 UTC | Merge branch 'updated' into gb_master | 22 May 2014, 18:56:40 UTC |
| 29ea46d | apregier | 22 May 2014, 18:30:44 UTC | New vaf interpreter | 22 May 2014, 18:55:10 UTC |
| 1775dbc | apregier | 22 May 2014, 18:29:56 UTC | Extract method to calculate vaf for multiple alleles | 22 May 2014, 18:55:09 UTC |
| f5eb56c | apregier | 22 May 2014, 17:28:03 UTC | Extract class VafCalculator | 22 May 2014, 18:55:09 UTC |
| 828a4cc | APipe Tester | 22 May 2014, 18:52:20 UTC | updated jenkins submodule to 1e8fe9c | 22 May 2014, 18:52:20 UTC |
| fc448ad | apregier | 22 May 2014, 17:14:13 UTC | Merge branch 'updated' into gb_master | 22 May 2014, 17:14:13 UTC |
| f54d1cd | apregier | 22 May 2014, 16:53:46 UTC | Make bam-readcount component base a mixin | 22 May 2014, 16:53:46 UTC |
| ea504ed | apregier | 22 May 2014, 16:44:36 UTC | Make WithSampleName a mixin | 22 May 2014, 16:44:36 UTC |
| 8081221 | apregier | 22 May 2014, 16:43:20 UTC | Make WithTranslatedInputs a mixin | 22 May 2014, 16:43:51 UTC |
| f9c04c7 | Jason Walker | 22 May 2014, 15:54:40 UTC | switch to using an array ref of default headers rather than attempting to sort the hash keys | 22 May 2014, 15:54:40 UTC |
| c141dd6 | Eddie Belter | 21 May 2014, 22:53:25 UTC | Import InstData: capture metrics from seq-grind sanitize to verify bam. | 21 May 2014, 22:57:38 UTC |
| 1638746 | Nathaniel Nutter | 21 May 2014, 22:54:58 UTC | show object display name instead of Perl ref | 21 May 2014, 22:55:23 UTC |
| acd6d66 | Nathaniel Nutter | 21 May 2014, 22:54:37 UTC | make option name match convention | 21 May 2014, 22:55:21 UTC |
| a3bde1f | apregier | 21 May 2014, 21:42:14 UTC | dbsnp interpreter for allele frequency | 21 May 2014, 21:42:14 UTC |
| cc842a8 | apregier | 21 May 2014, 21:14:36 UTC | Merge branch 'updated' into gb_master | 21 May 2014, 21:14:36 UTC |
| a3bc085 | apregier | 21 May 2014, 21:04:05 UTC | VerifyBamId uses CAF parser | 21 May 2014, 21:04:40 UTC |
| 069d35e | apregier | 21 May 2014, 18:58:22 UTC | New dbsnp af parser | 21 May 2014, 21:04:40 UTC |
| 85c4396 | apregier | 21 May 2014, 18:57:09 UTC | Adjust alleles to return the array This is so it behaves as expected in scalar context | 21 May 2014, 21:04:39 UTC |
| 3e36a52 | apregier | 21 May 2014, 15:47:35 UTC | Make known_variants input not is_many | 21 May 2014, 21:04:39 UTC |
| 4a1807b | apregier | 21 May 2014, 15:35:33 UTC | Made joinx expert specific to dbsnp | 21 May 2014, 21:04:38 UTC |
| 9209156 | apregier | 20 May 2014, 20:57:19 UTC | Remove unneeded code | 21 May 2014, 21:04:38 UTC |
| 05e1621 | Nathaniel Nutter | 21 May 2014, 19:38:52 UTC | add new research disk groups | 21 May 2014, 19:38:52 UTC |
| 22557ca | Thomas Mooney | 21 May 2014, 19:10:48 UTC | Look up the IDs to expunge using the key we were given to the hash. | 21 May 2014, 19:10:48 UTC |
| 5270a72 | Michael J. Kiwala | 21 May 2014, 18:24:14 UTC | Before calling ->name on workflow error validate that ->name can be called | 21 May 2014, 18:24:25 UTC |
| 6f44455 | APipe Tester | 21 May 2014, 12:19:50 UTC | Updated `gmt` tab completion. | 21 May 2014, 12:19:50 UTC |
| d21ce59 | APipe Tester | 21 May 2014, 12:19:01 UTC | Updated `genome` tab completion. | 21 May 2014, 12:19:01 UTC |
| 68bf795 | APipe Tester | 21 May 2014, 12:17:13 UTC | Updated class browser cache. | 21 May 2014, 12:17:13 UTC |
| 18a8080 | Nathaniel Nutter | 20 May 2014, 23:04:31 UTC | whitespace | 20 May 2014, 23:04:31 UTC |
| f49aaee | Nathaniel Nutter | 20 May 2014, 23:01:38 UTC | warn when files are missing since at least some are optional This is not necessarily the right thing to do but it is reverting assumptions that the opposite *was* the right thing to do and it was clearly not due to some files being optional, e.g. the error rate files. | 20 May 2014, 23:01:38 UTC |
| e755920 | Eddie Belter | 20 May 2014, 22:02:56 UTC | SX: sort command names when building command in external cmd base | 20 May 2014, 22:10:55 UTC |
| 3848f7d | Eddie Belter | 20 May 2014, 21:56:44 UTC | SX: add cmd for each flexbar version | 20 May 2014, 22:10:54 UTC |
| 2ab7da2 | Eddie Belter | 20 May 2014, 18:11:36 UTC | SX: remove vendor sub command | 20 May 2014, 22:10:54 UTC |
| 13232ee | Eddie Belter | 19 May 2014, 22:59:50 UTC | SX: add vendor/flexbar subcommand | 20 May 2014, 22:10:53 UTC |
| 801c06e | Eddie Belter | 19 May 2014, 22:59:36 UTC | SX: add vendor subcommand | 20 May 2014, 22:10:53 UTC |
| 4eb3e4d | Eddie Belter | 19 May 2014, 22:31:07 UTC | SX: rm flexbar version 2.4 | 20 May 2014, 22:10:52 UTC |
| 4e206b2 | dmorton | 20 May 2014, 21:50:04 UTC | Add missing test data | 20 May 2014, 21:50:24 UTC |
| 12585a7 | dmorton | 20 May 2014, 21:49:18 UTC | Bugfix wrong arguments passed to SUPER->__profile_errors__ | 20 May 2014, 21:50:24 UTC |
| f93cd20 | Nathaniel Nutter | 20 May 2014, 21:37:12 UTC | make package name match path so this shows up under the parent's --help | 20 May 2014, 21:45:22 UTC |
| a07137d | Anthony Brummett | 20 May 2014, 20:59:34 UTC | extract method to compare build output directories by pathname | 20 May 2014, 21:39:46 UTC |
| 5915c6a | Anthony Brummett | 20 May 2014, 20:54:41 UTC | these can be called as class methods | 20 May 2014, 21:39:46 UTC |
| 41f9af5 | Anthony Brummett | 20 May 2014, 20:52:16 UTC | use the string-centric functions for dealing with these directory names | 20 May 2014, 21:39:45 UTC |
| d5ad426 | Anthony Brummett | 20 May 2014, 20:42:40 UTC | extract method to compare the output files of two builds | 20 May 2014, 21:39:44 UTC |
| d9b2e9e | Anthony Brummett | 20 May 2014, 20:35:22 UTC | extract function to convert a canonical path to one relative to another | 20 May 2014, 21:39:44 UTC |
| 3c161dc | Anthony Brummett | 20 May 2014, 20:30:22 UTC | rename variable $dir => $base_dir | 20 May 2014, 21:39:43 UTC |
| d5393b1 | Anthony Brummett | 20 May 2014, 20:27:47 UTC | extract function to find files under a named directory | 20 May 2014, 21:39:43 UTC |
| 893acaf | Gabriel Sanderson | 20 May 2014, 21:23:13 UTC | RunsAnnotation checks if annotation plans are valid on creation. RunsAnnotation now has __profile_errors that checks the validity of annotation plans. Refactored out _annotation_plan_search_dir for test overriding. | 20 May 2014, 21:27:07 UTC |
| 965969c | Gabriel Sanderson | 20 May 2014, 19:46:42 UTC | Avoid using $@ directly | 20 May 2014, 21:27:05 UTC |
| d2c1a5a | Gabriel Sanderson | 20 May 2014, 19:25:15 UTC | ReporterPlans can now return requires_experts (by asking children) | 20 May 2014, 21:27:03 UTC |
| 2968824 | Nathaniel Nutter | 20 May 2014, 20:49:56 UTC | specify the view for models instead of using default model status view On a smaller model group (~20 models) this resulted in a 20% reduction in SQL queries but on a larger model group this resulted in a 66% reduction in SQL queries. From my testing it produces the same view. | 20 May 2014, 21:01:47 UTC |
| b32988b | Nathaniel Nutter | 19 May 2014, 21:59:31 UTC | avoid uninitialized value warnings | 20 May 2014, 21:01:45 UTC |
| f09df58 | apregier | 20 May 2014, 20:53:36 UTC | Merge branch 'updated' into gb_master | 20 May 2014, 20:53:36 UTC |
| 6ddeec9 | apregier | 20 May 2014, 20:45:20 UTC | rsid interpreter | 20 May 2014, 20:45:20 UTC |
| a57234b | apregier | 20 May 2014, 20:45:02 UTC | Fix usage documentation | 20 May 2014, 20:45:02 UTC |
| 4af05b6 | apregier | 20 May 2014, 20:04:41 UTC | Merge branch 'updated' into gb_master | 20 May 2014, 20:04:41 UTC |
| 099dc2e | apregier | 20 May 2014, 19:40:09 UTC | n-callers filter | 20 May 2014, 19:57:59 UTC |
| 583d90d | Susanna Siebert | 20 May 2014, 19:36:31 UTC | clean up test data | 20 May 2014, 19:38:10 UTC |
| a6b6acd | Susanna Siebert | 20 May 2014, 19:30:28 UTC | don't use the second (custom) reference, use build37 | 20 May 2014, 19:38:08 UTC |
| 4f476f7 | Susanna Siebert | 20 May 2014, 18:54:48 UTC | remove reinstall of bam_path since it's not needed with shortcutting | 20 May 2014, 19:38:07 UTC |
| c2e9e8d | Susanna Siebert | 20 May 2014, 18:49:59 UTC | Create software result objects for clip overlap to allow shortcutting | 20 May 2014, 19:38:06 UTC |
| 71a0360 | Susanna Siebert | 20 May 2014, 18:41:10 UTC | Create software result objects for gatk to allow shortcutting - certain tests fail because intermediate results don't exist | 20 May 2014, 19:38:05 UTC |
| f625e19 | Susanna Siebert | 20 May 2014, 18:37:50 UTC | Edit for clarity | 20 May 2014, 19:38:05 UTC |
| 1b45bfd | Gabriel Sanderson | 20 May 2014, 18:28:59 UTC | Refactor __errors__ to examine different error types. __errors__ now calls __plan_errors__, __object_errors__, __class_errors__, and __child_errors__. | 20 May 2014, 18:31:14 UTC |
| 4cfca2c | Gabriel Sanderson | 20 May 2014, 18:28:00 UTC | Reporter/WithHeader - Return errors instead of dying | 20 May 2014, 18:31:13 UTC |
| 842e397 | Gabriel Sanderson | 20 May 2014, 18:27:26 UTC | Test helpers out of date - experts do not have properties directly | 20 May 2014, 18:31:12 UTC |
| 8bcc1e5 | Gabriel Sanderson | 20 May 2014, 18:26:14 UTC | Test data was out of date - added file_name to reporters. | 20 May 2014, 18:31:12 UTC |
| f07be66 | Gabriel Sanderson | 19 May 2014, 21:55:54 UTC | Refactor logic from validate_with_plan_params into plan_params_errors which returns UR tags | 20 May 2014, 18:31:11 UTC |
| 197f604 | Gabriel Sanderson | 19 May 2014, 21:50:50 UTC | remove unused param pass for __errors__ | 20 May 2014, 18:31:10 UTC |
| 691528c | Gabriel Sanderson | 16 May 2014, 22:51:06 UTC | Remove validate_inputs, inherit from ComponentBase to avoid code duplication | 20 May 2014, 18:31:09 UTC |
| ad92350 | Gabriel Sanderson | 16 May 2014, 22:46:38 UTC | documentation | 20 May 2014, 18:31:09 UTC |
| b5a1b23 | Gabriel Sanderson | 16 May 2014, 22:41:35 UTC | remove duplicate code in validate_self, call SUPER instead. | 20 May 2014, 18:31:08 UTC |
| 6694caa | Gabriel Sanderson | 16 May 2014, 22:38:37 UTC | eliminate validate_params, refactor up validate | 20 May 2014, 18:31:07 UTC |
| fdde9b9 | Gabriel Sanderson | 16 May 2014, 22:33:41 UTC | Refactored up validate_self | 20 May 2014, 18:31:07 UTC |
| 0e8f4ed | Gabriel Sanderson | 16 May 2014, 22:27:37 UTC | Once again check specific error output. | 20 May 2014, 18:31:06 UTC |
| 3508b6a | Gabriel Sanderson | 16 May 2014, 22:18:15 UTC | Call ->object more safely in ReporterPlan | 20 May 2014, 18:31:05 UTC |
| f53dbb5 | Gabriel Sanderson | 16 May 2014, 22:10:07 UTC | remove now unused test_bad_plan_old | 20 May 2014, 18:31:05 UTC |
| e310163 | Gabriel Sanderson | 16 May 2014, 22:04:42 UTC | no longer validate SUPER in self, __errors__ does that work | 20 May 2014, 18:31:04 UTC |
| c5bad2b | Gabriel Sanderson | 16 May 2014, 22:03:37 UTC | WithHeader.pm now implements __errors__ | 20 May 2014, 18:31:03 UTC |
| a5bd2e9 | Gabriel Sanderson | 16 May 2014, 21:55:47 UTC | Plan/Base.pm now uses __errors__. No longer have to validate SUPER or children in validate_self, because errors will gather super and children's errors. | 20 May 2014, 18:31:03 UTC |
| 14cf057 | Gabriel Sanderson | 16 May 2014, 21:32:00 UTC | Plan.pm updates to use __errors__. Plan.pm still calls SUPER::validate_self, should eliminate this in the next commit. Plan-validate.t no longer relies on throws_ok, but does not yet check for contents of __errors__ | 20 May 2014, 18:31:02 UTC |
