| ac241ac | Feiyu Du | 11 June 2014, 18:21:13 UTC | bug fix to copy tabix index over to build dir | 11 June 2014, 18:21:13 UTC |
| dc981b4 | Adam Coffman | 11 June 2014, 15:11:23 UTC | bless clinseq build with dgidb source update | 11 June 2014, 15:11:23 UTC |
| 62652c2 | apregier | 10 June 2014, 21:59:27 UTC | Merge branch 'updated' into gb_master | 10 June 2014, 21:59:27 UTC |
| f27feb3 | apregier | 10 June 2014, 21:51:20 UTC | Add Damaging sift/polyphen filter | 10 June 2014, 21:51:20 UTC |
| 9f64707 | apregier | 10 June 2014, 17:51:55 UTC | Merge branch 'updated' into gb_master | 10 June 2014, 17:51:55 UTC |
| 245f7c6 | apregier | 10 June 2014, 17:30:22 UTC | Interpreter also provides sift,polyphen, and condel | 10 June 2014, 17:39:01 UTC |
| 25f5323 | apregier | 10 June 2014, 17:29:45 UTC | Change function name to reflect return value | 10 June 2014, 17:39:00 UTC |
| c9f0f1e | Thomas Mooney | 10 June 2014, 15:27:38 UTC | New command to monitor library and sample renames. | 10 June 2014, 15:27:38 UTC |
| a19b475 | Thomas Mooney | 10 June 2014, 13:30:27 UTC | Remove extra ":" in doc text. | 10 June 2014, 13:30:27 UTC |
| 2fa85dd | APipe Tester | 10 June 2014, 12:19:00 UTC | Updated `gmt` tab completion. | 10 June 2014, 12:19:00 UTC |
| b5c8642 | APipe Tester | 10 June 2014, 12:18:14 UTC | Updated `genome` tab completion. | 10 June 2014, 12:18:14 UTC |
| e47e0be | Avinash Ramu | 10 June 2014, 02:20:31 UTC | update clinseq-blessed This build has changes to DGIdb. An additional source is being added. | 10 June 2014, 02:20:31 UTC |
| e3b4a0d | Avinash Ramu | 09 June 2014, 20:36:42 UTC | update CNV plotting and ROC metrics | 10 June 2014, 02:18:14 UTC |
| 35c24eb | Avinash Ramu | 08 June 2014, 05:58:39 UTC | update stats plot | 10 June 2014, 02:18:13 UTC |
| c037747 | Avinash Ramu | 05 June 2014, 19:53:56 UTC | add tool for plotting clinseq stats | 10 June 2014, 02:18:13 UTC |
| e3a6f05 | Eddie Belter | 09 June 2014, 22:49:27 UTC | Sample import: sort sample/ind attr names | 09 June 2014, 22:49:49 UTC |
| c77a9d3 | Eddie Belter | 09 June 2014, 22:40:01 UTC | Sample Import: allow more EMBL-EBI names | 09 June 2014, 22:49:48 UTC |
| e691c30 | Eddie Belter | 09 June 2014, 22:39:11 UTC | Sample Import: add is_optioonal to calculated importer properties to avoid command errors | 09 June 2014, 22:49:48 UTC |
| eb1d723 | Eddie Belter | 09 June 2014, 21:24:23 UTC | Sample Import: cleanup getting property meta from entity | 09 June 2014, 22:49:47 UTC |
| af5512d | Eddie Belter | 09 June 2014, 18:54:21 UTC | Sample import: rm unused storing of properties | 09 June 2014, 22:49:46 UTC |
| c833dc4 | Eddie Belter | 06 June 2014, 22:08:45 UTC | Sample import test update | 09 June 2014, 22:49:45 UTC |
| 9305f1c | Dave Larson | 09 June 2014, 21:44:16 UTC | remove readlength error message as it is no longer needed. Also add error message if an alignment result is missing. | 09 June 2014, 21:44:35 UTC |
| aa23dea | Avinash Ramu | 09 June 2014, 21:01:09 UTC | update clinseq blessed | 09 June 2014, 21:06:40 UTC |
| 3001cce | Avinash Ramu | 09 June 2014, 21:00:05 UTC | update tests | 09 June 2014, 21:06:40 UTC |
| 3fabb48 | Avinash Ramu | 08 June 2014, 06:00:15 UTC | skip LIMS reports for now | 09 June 2014, 21:06:39 UTC |
| 10b0ee6 | APipe Tester | 09 June 2014, 15:32:06 UTC | updated jenkins submodule to da389bf | 09 June 2014, 15:32:06 UTC |
| 8091f3a | Nathaniel Nutter | 05 June 2014, 21:55:28 UTC | remove 'other' permission bits This is only a half-measure to reflect the new policy that 'other' shouldn't have access to Genome or its output. | 06 June 2014, 19:58:43 UTC |
| 7f922fa | Nathaniel Nutter | 05 June 2014, 21:37:04 UTC | remove set_file_permissions and set_directory_permissions Remove set_file_permissions and set_directory_permissions to be replaced with 'mode' and File::Find::Rule. | 06 June 2014, 19:58:39 UTC |
| 39ea406 | Nathaniel Nutter | 05 June 2014, 21:33:15 UTC | remove unused function | 06 June 2014, 19:58:38 UTC |
| d8387a2 | Gabriel Sanderson | 06 June 2014, 18:49:47 UTC | Updated tier 1 consequence types per cmiller. | 06 June 2014, 18:50:52 UTC |
| d18c6c7 | Yevgeniy Gindin | 06 June 2014, 15:43:51 UTC | Added more tests | 06 June 2014, 15:43:51 UTC |
| e7eda0a | APipe Tester | 06 June 2014, 12:17:55 UTC | Updated `gmt` tab completion. | 06 June 2014, 12:17:55 UTC |
| 9b5f6f7 | APipe Tester | 06 June 2014, 12:17:13 UTC | Updated `genome` tab completion. | 06 June 2014, 12:17:13 UTC |
| cb04235 | APipe Tester | 06 June 2014, 12:15:36 UTC | Updated class browser cache. | 06 June 2014, 12:15:36 UTC |
| 4ba0997 | Avinash Ramu | 06 June 2014, 05:08:33 UTC | Rename file in diff-ignore as well. | 06 June 2014, 05:08:33 UTC |
| 7612b75 | Avinash Ramu | 05 June 2014, 21:47:41 UTC | rename summarize-builds | 05 June 2014, 21:48:48 UTC |
| 557d79c | ygindin | 05 June 2014, 21:38:21 UTC | fixed mis-placed use statement | 05 June 2014, 21:38:21 UTC |
| 8728152 | ygindin | 05 June 2014, 21:21:11 UTC | small change | 05 June 2014, 21:21:11 UTC |
| 7a545b4 | ygindin | 05 June 2014, 21:18:02 UTC | Added ProcessManualReview | 05 June 2014, 21:18:02 UTC |
| 12d6dc2 | Gabriel Sanderson | 05 June 2014, 21:02:23 UTC | Added Tier 1 filter and related test. The tier 1 consequence types list needs to be updated, this is just a handful of valid types so far. | 05 June 2014, 21:03:30 UTC |
| 86ecfbb | Nathaniel Nutter | 05 June 2014, 20:35:37 UTC | remove write instead of setting absolute permissions Setting absolute permissions is often not the correct thing to do because it doesn't account for other bits the file/directory might have, e.g. setgid, or executable. So, for example, instead of setting thing readonly by doing `chmod 444` one could instead do `chmod a-w`. | 05 June 2014, 20:41:00 UTC |
| 775c235 | Nathaniel Nutter | 05 June 2014, 18:54:50 UTC | remove commented out code | 05 June 2014, 20:40:58 UTC |
| 5574852 | Nathaniel Nutter | 04 June 2014, 21:05:25 UTC | fix importing a function into base_class causing result class to break This is super weird. Why would a parent class override a subclass? I hope it's safe to limit this behavior to just properties. Importing 'mode' into Genome::SoftwareResult::Stageable broke Genome::Model::Tools::Htseq::Count because that class has a property named 'mode'. | 05 June 2014, 20:40:57 UTC |
| 8254768 | Nathaniel Nutter | 03 June 2014, 22:27:50 UTC | switch from glob to File::Find::Rule | 05 June 2014, 20:40:56 UTC |
| 7e366ab | Nathaniel Nutter | 03 June 2014, 22:15:51 UTC | include path in error message | 05 June 2014, 20:40:55 UTC |
| 0c587bd | Nathaniel Nutter | 03 June 2014, 21:22:01 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:54 UTC |
| 8eb8b24 | Nathaniel Nutter | 03 June 2014, 21:18:26 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:53 UTC |
| 4dc7b43 | Nathaniel Nutter | 03 June 2014, 21:17:34 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:52 UTC |
| 0785c43 | Nathaniel Nutter | 03 June 2014, 21:14:34 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:51 UTC |
| 4ea3c1a | Nathaniel Nutter | 03 June 2014, 21:13:14 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:50 UTC |
| 2074625 | Nathaniel Nutter | 03 June 2014, 21:12:16 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:49 UTC |
| 91a0613 | ygindin | 05 June 2014, 16:03:07 UTC | Fixed relative paths issue | 05 June 2014, 16:03:07 UTC |
| 648d2f1 | apregier | 05 June 2014, 15:08:09 UTC | Merge branch 'updated' into gb_master | 05 June 2014, 15:08:09 UTC |
| 50cec18 | apregier | 04 June 2014, 22:09:45 UTC | Use class method instead of object method | 05 June 2014, 15:06:56 UTC |
| dab295c | apregier | 04 June 2014, 22:09:21 UTC | Use class method instead of object method | 05 June 2014, 15:06:56 UTC |
| 82c61a1 | apregier | 04 June 2014, 22:08:46 UTC | Add class method to get sample_name_in_vcf | 05 June 2014, 15:06:55 UTC |
| fac9c68 | apregier | 03 June 2014, 19:21:00 UTC | Use sample->name_in_vcf | 05 June 2014, 15:06:54 UTC |
| 41f27a6 | apregier | 03 June 2014, 19:20:39 UTC | Use sample->name_in_vcf | 05 June 2014, 15:06:54 UTC |
| b1fd14d | apregier | 03 June 2014, 19:19:56 UTC | Move method to translate tcga names into sample class | 05 June 2014, 15:06:53 UTC |
| c1a7989 | APipe Tester | 05 June 2014, 12:17:44 UTC | Updated `gmt` tab completion. | 05 June 2014, 12:17:44 UTC |
| f643858 | APipe Tester | 05 June 2014, 12:17:02 UTC | Updated `genome` tab completion. | 05 June 2014, 12:17:02 UTC |
| fc3c116 | APipe Tester | 05 June 2014, 12:15:30 UTC | Updated class browser cache. | 05 June 2014, 12:15:30 UTC |
| bfba28e | Gabriel Sanderson | 04 June 2014, 22:39:42 UTC | refactor fpkm_for_genotype_allele into FpkmBase. I considered just making the MinFpkm filter inherit from the FpkmInterpreter, but this would remove our native 'soft filtering' ability by overwriting the interpret_entry method from Filter/Base. | 04 June 2014, 22:39:42 UTC |
| 8306fdf | Gabriel Sanderson | 04 June 2014, 22:31:15 UTC | Added MinFpkm filter and test. | 04 June 2014, 22:31:38 UTC |
| 423887a | Travis Abbott | 04 June 2014, 21:31:18 UTC | tool to compare bed/bedpe sv files to true positives | 04 June 2014, 21:31:18 UTC |
| 9ad9d0c | Travis Abbott | 04 June 2014, 21:05:24 UTC | fix breakdancer-to-bed when not writing all sv types everything was ok when processing all SV types, but crashing when doing only a subset | 04 June 2014, 21:05:24 UTC |
| 6265d87 | Travis Abbott | 04 June 2014, 20:43:32 UTC | add sv-sim code to run breakdancer & produce bed/bedpe files | 04 June 2014, 20:43:32 UTC |
| ac24d94 | Susanna Siebert | 04 June 2014, 20:18:49 UTC | move FPKM expert and interpreter to VariantReporting namespace | 04 June 2014, 20:18:49 UTC |
| e0182e0 | Susanna Siebert | 04 June 2014, 18:33:24 UTC | subtest for heterozygous, non-reference genotype | 04 June 2014, 19:42:25 UTC |
| c797764 | Susanna Siebert | 04 June 2014, 18:27:38 UTC | handle interpreting of FPKM values on a per genotype allele basis | 04 June 2014, 19:42:24 UTC |
| cd51d4c | Susanna Siebert | 04 June 2014, 17:47:16 UTC | handle FPKM value on a per genotype allele basis | 04 June 2014, 19:42:23 UTC |
| 4a505a5 | Susanna Siebert | 04 June 2014, 13:48:57 UTC | pull out test data version | 04 June 2014, 19:42:23 UTC |
| 3209079 | Gabriel Sanderson | 03 June 2014, 22:44:39 UTC | Added FpkmInterpreter - still need to account for multiple values | 04 June 2014, 19:42:22 UTC |
| cef6d7e | Gabriel Sanderson | 03 June 2014, 22:00:01 UTC | Move WithSampleName up so interpreters can use it | 04 June 2014, 19:33:32 UTC |
| 574c5b1 | Susanna Siebert | 03 June 2014, 19:41:56 UTC | test file for FPKM Run module | 04 June 2014, 19:25:33 UTC |
| c0b944e | Susanna Siebert | 03 June 2014, 19:41:26 UTC | fixed some errors in file handling | 04 June 2014, 19:25:32 UTC |
| ac7b914 | Susanna Siebert | 02 June 2014, 18:26:43 UTC | added test for intergenic transcript status message | 04 June 2014, 19:25:32 UTC |
| 09c306e | Susanna Siebert | 02 June 2014, 18:14:19 UTC | test for AnnotateWithFpkm | 04 June 2014, 19:25:31 UTC |
| 7e2101c | Susanna Siebert | 30 May 2014, 20:37:33 UTC | Make FPKM a sample field on the vcf instead of an info field | 04 June 2014, 19:25:30 UTC |
| 335e4d3 | Susanna Siebert | 30 May 2014, 19:13:32 UTC | handle multiple FPKM entries for a gene and take FPKM status into account | 04 June 2014, 19:25:29 UTC |
| 32b7519 | Susanna Siebert | 30 May 2014, 19:12:35 UTC | add handling for intergenic transcripts | 04 June 2014, 19:25:29 UTC |
| 307c450 | Susanna Siebert | 30 May 2014, 18:18:24 UTC | Fix the way the FPKM info field is added | 04 June 2014, 19:25:28 UTC |
| d30e79d | Gabriel Sanderson | 29 May 2014, 22:50:42 UTC | Added partially-complete modules for the FPKM expert. Adaptor - Works. Should be done, unless we need other properties later. Expert.pm, Run.pm, and RunResult.pm - Works, very small modules anyways. Expert.t - Works, test passes but the expected vcf is not yet correct (No FPKM values are added, gmt vcf annotate tool probably does not work yet). | 04 June 2014, 19:25:27 UTC |
| 6aa14d3 | Gabriel Sanderson | 29 May 2014, 22:49:46 UTC | Added a helper method to get a test build with VEP values present in the vcf | 04 June 2014, 19:25:27 UTC |
| 6f99ab4 | Gabriel Sanderson | 29 May 2014, 22:45:15 UTC | Added a helper method to get a test build that has vcfs with vep annotations. | 04 June 2014, 19:25:17 UTC |
| 1e15169 | Gabriel Sanderson | 29 May 2014, 22:40:13 UTC | DO NOT PUSH -- temporarily comment out dying when we get multiple fpkm values for the same gene. This is needed to keep testing while we wait to hear from Chris and Jasreet | 04 June 2014, 19:24:38 UTC |
| 8429e16 | Gabriel Sanderson | 29 May 2014, 22:38:57 UTC | Added a tool to add FPKM annotations to a vcf file. The Vcf file must be previously annotated with VEP with the option --pick. TODO: does not seem to be fully functional yet, FPKM annotations are not added to each variant, but the header is changed. | 04 June 2014, 19:24:37 UTC |
| 7f3efd1 | Chris Miller | 04 June 2014, 18:28:03 UTC | adding a sanity check to prevent double headers on the corrected file. This causes all sorts of nastyness in R, which will try to compare strings instead of numbers for that column | 04 June 2014, 18:28:08 UTC |
| 03e446a | Chris Miller | 04 June 2014, 16:11:32 UTC | adding some debugging info to the wrapper | 04 June 2014, 18:28:07 UTC |
| e642a89 | Nathaniel Nutter | 04 June 2014, 14:56:12 UTC | convert calculated disk_allocation to a reverse_as property | 04 June 2014, 16:30:37 UTC |
| ef53cf2 | Nathaniel Nutter | 04 June 2014, 15:36:52 UTC | symlink can't be made until after original is removed | 04 June 2014, 16:30:35 UTC |
| 2d15dfd | Feiyu Du | 04 June 2014, 16:30:13 UTC | add ref_seq_build check | 04 June 2014, 16:30:13 UTC |
| 9dcde4f | Feiyu Du | 04 June 2014, 15:44:09 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 June 2014, 15:44:09 UTC |
| 8c81229 | Feiyu Du | 04 June 2014, 15:44:02 UTC | escape () for some sample name | 04 June 2014, 15:44:02 UTC |
| efa69a2 | Thomas Mooney | 04 June 2014, 15:37:10 UTC | Remove outdated/erroneous information from help text. | 04 June 2014, 15:37:10 UTC |
| 23f753f | Thomas Mooney | 04 June 2014, 15:30:59 UTC | Remove non-functional cleanup option and deletion code. | 04 June 2014, 15:30:59 UTC |
| 6ede498 | Thomas Mooney | 04 June 2014, 15:09:17 UTC | Merge branch 'iterative-qc'. Updates to the iterative qc tool to get it working again plus a little cleanup. | 04 June 2014, 15:09:17 UTC |
| 15e3bc4 | APipe Tester | 04 June 2014, 12:18:00 UTC | Updated `gmt` tab completion. | 04 June 2014, 12:18:00 UTC |
| b8dc9c4 | APipe Tester | 04 June 2014, 12:17:20 UTC | Updated `genome` tab completion. | 04 June 2014, 12:17:20 UTC |
| 1aec9d7 | APipe Tester | 04 June 2014, 12:15:46 UTC | Updated class browser cache. | 04 June 2014, 12:15:46 UTC |
