| 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 |
| d90a946 | Gabriel Sanderson | 16 May 2014, 20:31:25 UTC | ReporterPlan now uses __errors__. Plan-validate.t has less specific error checking for now. | 20 May 2014, 18:31:01 UTC |
| d24dc03 | Gabriel Sanderson | 15 May 2014, 21:23:50 UTC | Refactor validate_inputs from BamReadcount/Run.pm to Expert/CommandBase.pm | 20 May 2014, 18:31:00 UTC |
| 9b5a61b | Gabriel Sanderson | 15 May 2014, 21:19:28 UTC | Refactor validate_inputs logic into __errors__ | 20 May 2014, 18:30:59 UTC |
| ee176da | Thomas Mooney | 20 May 2014, 17:25:39 UTC | Don't fail alignment when we can't remove the IntermediateAlignmentResult. Keep an inactive user link to the IAR in case it isn't deleted. | 20 May 2014, 17:25:39 UTC |
| 647b324 | APipe Tester | 20 May 2014, 12:20:36 UTC | Updated `genome` tab completion. | 20 May 2014, 12:20:36 UTC |
| 0fbf225 | APipe Tester | 20 May 2014, 12:18:47 UTC | Updated class browser cache. | 20 May 2014, 12:18:47 UTC |
| 5365b6d | Feiyu Du | 19 May 2014, 22:11:44 UTC | run SpliceJunctionSummary specifically on tophat alignment | 19 May 2014, 22:11:44 UTC |
| eaafd94 | Nathaniel Nutter | 19 May 2014, 21:28:12 UTC | remove unused line | 19 May 2014, 21:28:32 UTC |
| b024645 | Nathaniel Nutter | 19 May 2014, 21:27:11 UTC | it seems like default implies optional but it doesn't so make explicit This fixes what looks like an invalid workflow due to missing inputs since the inputs have default values but aren't marked as optional. | 19 May 2014, 21:28:31 UTC |
| ef39c54 | Nathaniel Nutter | 19 May 2014, 21:24:47 UTC | since builds is_many should specify as array While Workflow might support passing singular items into is_many inputs it is better if the thing that has knowledege about the inputs (the model) specifies a list with one element. Flow does not wrap single elements in a list. | 19 May 2014, 21:28:29 UTC |
| 31c7d31 | apregier | 19 May 2014, 21:13:18 UTC | Removed vep params | 19 May 2014, 21:13:18 UTC |
| 6e3f7b3 | apregier | 19 May 2014, 19:36:31 UTC | Remove parameterization from vep so things always get run | 19 May 2014, 21:09:14 UTC |
| 36e2532 | apregier | 19 May 2014, 18:07:49 UTC | Added new outputs to vep interpreter | 19 May 2014, 20:29:33 UTC |
| b6369a3 | apregier | 19 May 2014, 16:57:11 UTC | New contains-tag filter | 19 May 2014, 20:29:33 UTC |
| 40d4d9e | apregier | 19 May 2014, 20:23:44 UTC | Keep using IPC::Run | 19 May 2014, 20:23:44 UTC |
| d21eb85 | Thomas Mooney | 19 May 2014, 20:03:39 UTC | Provide a reason when abandoning the builds. | 19 May 2014, 20:03:39 UTC |
| 729c25e | APipe Tester | 19 May 2014, 19:44:54 UTC | updated graphite submodule to be02103 | 19 May 2014, 19:44:54 UTC |
| 15a6f83 | dmorton | 19 May 2014, 17:19:21 UTC | die when no API path can be found This makes it so that less boilerplate is needed by consumers of this method as well as being more consistent with the way Sys->shellcmd works. | 19 May 2014, 18:06:38 UTC |
| 92d667d | dmorton | 19 May 2014, 17:18:30 UTC | Use Genome::Sys->shellcmd instead of IPC::Run 1) for status logging 2) for input/output file validation | 19 May 2014, 18:06:38 UTC |
| eefd30b | dmorton | 13 May 2014, 23:10:50 UTC | Invalid annotation plans cause builds to be unstartable | 19 May 2014, 18:06:37 UTC |
| 00eaeb0 | dmorton | 13 May 2014, 22:22:31 UTC | Vep correctly annotates multiple alternate alleles | 19 May 2014, 18:06:37 UTC |
| a2a369b | dmorton | 13 May 2014, 02:21:23 UTC | Fix imports related to File::Vcf::Differ | 19 May 2014, 18:06:37 UTC |
| 001833e | dmorton | 13 May 2014, 02:16:40 UTC | Add SplitAlternateAlleles and test This command splits vcf lines into multiple lines (one per alternate allele) and clears INFO fields. | 19 May 2014, 18:06:37 UTC |
| 730cd28 | dmorton | 12 May 2014, 22:58:56 UTC | Remove spurious execution return value checking | 19 May 2014, 18:06:37 UTC |
| e331d8b | dmorton | 12 May 2014, 20:23:44 UTC | Replace temp with methods | 19 May 2014, 18:06:37 UTC |
| e2bc1c7 | dmorton | 12 May 2014, 20:17:15 UTC | Replace temp with method (vep_params) | 19 May 2014, 18:06:37 UTC |
| 0d64f89 | dmorton | 12 May 2014, 20:16:37 UTC | Replace temp with method (custom_annotation_inputs) | 19 May 2014, 18:06:37 UTC |
| 99df226 | Avinash Ramu | 19 May 2014, 02:52:11 UTC | update clin-seq blessed | 19 May 2014, 02:52:42 UTC |
| 19c1d66 | Avinash Ramu | 19 May 2014, 01:43:45 UTC | update getvariant sources to handle mutect | 19 May 2014, 02:52:40 UTC |
| 3083d30 | Avinash Ramu | 16 May 2014, 17:11:02 UTC | extract method | 19 May 2014, 02:52:37 UTC |
| 8162c78 | Avinash Ramu | 16 May 2014, 16:04:55 UTC | refactor write output file | 19 May 2014, 02:52:37 UTC |
| 1f741c7 | Avinash Ramu | 16 May 2014, 15:20:34 UTC | minor refactor | 19 May 2014, 02:52:36 UTC |
| eb3fd72 | Avinash Ramu | 14 May 2014, 21:47:42 UTC | remove unused function | 19 May 2014, 02:52:36 UTC |
| d849156 | Avinash Ramu | 14 May 2014, 21:37:15 UTC | update description for cnv plot tool | 19 May 2014, 02:52:35 UTC |
| a19b00d | Adam Coffman | 16 May 2014, 20:12:31 UTC | make is_capture return explicit 1 or 0 | 16 May 2014, 20:12:31 UTC |
| 377b438 | Adam Coffman | 16 May 2014, 19:43:08 UTC | analysis project deletes now cascade | 16 May 2014, 19:43:08 UTC |
| b026682 | APipe Tester | 16 May 2014, 16:49:24 UTC | updated jenkins submodule to 5eb7e15 | 16 May 2014, 16:49:24 UTC |
| e7b8a5a | APipe Tester | 16 May 2014, 14:54:38 UTC | updated ur submodule to 48f2b46 | 16 May 2014, 14:54:38 UTC |
| 2d60b31 | APipe Tester | 16 May 2014, 12:19:50 UTC | Updated `gmt` tab completion. | 16 May 2014, 12:19:50 UTC |
| 774b570 | APipe Tester | 16 May 2014, 12:19:05 UTC | Updated `genome` tab completion. | 16 May 2014, 12:19:05 UTC |
| 151af66 | APipe Tester | 16 May 2014, 12:17:28 UTC | Updated class browser cache. | 16 May 2014, 12:17:28 UTC |
| 77e4543 | APipe Tester | 15 May 2014, 22:59:57 UTC | updated ur submodule to b35b1b1 | 15 May 2014, 22:59:57 UTC |
| fc9a49f | Chris Miller | 15 May 2014, 21:27:28 UTC | adding --clean-output option to avoid all of the symlinking junk. I'd prefer that it be clean by default with the option to turn on symlinks, but I suspect that would require changing dozens of places in the codebase | 15 May 2014, 22:24:39 UTC |
| 0989505 | Eddie Belter | 15 May 2014, 22:13:19 UTC | GM: add logic to test factory to set genotype file | 15 May 2014, 22:13:28 UTC |
| 51174fe | Dave Larson | 15 May 2014, 21:00:37 UTC | Append change frequency instead of prepend | 15 May 2014, 21:01:04 UTC |
| a1804a3 | Adam Coffman | 15 May 2014, 20:53:01 UTC | fall back on empty string rather than undef to avoid warnings | 15 May 2014, 20:53:01 UTC |
| b0b5e0e | Eddie Belter | 15 May 2014, 20:30:16 UTC | InstData GM: add snp hash getting to meethods installed to imported; misc cleanup | 15 May 2014, 20:30:35 UTC |
| 1b1e2dc | Eddie Belter | 15 May 2014, 19:57:15 UTC | InstData GM: move genotype_file methods to Microarray class; install genotype file methods from Microarray into Imported | 15 May 2014, 20:30:33 UTC |
