| 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 |
| 3a82e98 | Avinash Ramu | 03 June 2014, 22:19:32 UTC | don't diff jpegs | 03 June 2014, 22:19:53 UTC |
| 6db380e | ygindin | 03 June 2014, 22:15:47 UTC | Add OncoPrint | 03 June 2014, 22:15:47 UTC |
| fe901d0 | Avinash Ramu | 03 June 2014, 21:54:01 UTC | update clin-seq blessed | 03 June 2014, 21:56:46 UTC |
| ee90fb6 | Avinash Ramu | 03 June 2014, 21:53:14 UTC | update test data | 03 June 2014, 21:56:45 UTC |
| 9645148 | Avinash Ramu | 03 June 2014, 19:43:38 UTC | undo test change | 03 June 2014, 21:56:45 UTC |
| 139e4e6 | Avinash Ramu | 03 June 2014, 19:41:47 UTC | get lrr from function | 03 June 2014, 21:56:44 UTC |
| 5364671 | Avinash Ramu | 03 June 2014, 16:29:43 UTC | add checks to bam-qc tools | 03 June 2014, 21:56:44 UTC |
| 83ccc9f | Avinash Ramu | 03 June 2014, 16:28:32 UTC | add cnview to exome-cnv | 03 June 2014, 21:56:43 UTC |
| 9693d2d | Nathaniel Nutter | 03 June 2014, 20:19:42 UTC | remove write instead of setting absolute permissions | 03 June 2014, 21:03:15 UTC |
| 7321a94 | Nathaniel Nutter | 03 June 2014, 20:30:41 UTC | remove write instead of setting absolute permissions | 03 June 2014, 21:02:26 UTC |
| 8f21491 | Nathaniel Nutter | 03 June 2014, 20:03:36 UTC | remove write instead of setting absolute permissions | 03 June 2014, 21:01:44 UTC |
| 35429fd | Nathaniel Nutter | 02 June 2014, 19:59:31 UTC | don't need to check regex first | 03 June 2014, 21:00:58 UTC |
| 7ab1e28 | Nathaniel Nutter | 03 June 2014, 21:00:16 UTC | remove write instead of setting absolute permissions | 03 June 2014, 21:00:16 UTC |
| 1cb4d2c | Nathaniel Nutter | 03 June 2014, 20:59:26 UTC | make setgid optional, transient was still preventing commit | 03 June 2014, 20:59:26 UTC |
| b74b244 | Thomas Mooney | 03 June 2014, 20:27:43 UTC | Add api v5 with Picard 1.113 | 03 June 2014, 20:27:43 UTC |
| 4291332 | Feiyu Du | 03 June 2014, 19:28:04 UTC | add ref_seq_build check | 03 June 2014, 19:28:04 UTC |
| 3d203f4 | APipe Tester | 03 June 2014, 17:19:22 UTC | updated jenkins submodule to 7d04db6 | 03 June 2014, 17:19:22 UTC |
| 2a0f3f4 | APipe Tester | 03 June 2014, 12:17:31 UTC | Updated `genome` tab completion. | 03 June 2014, 12:17:31 UTC |
| 9fa4454 | APipe Tester | 03 June 2014, 12:15:53 UTC | Updated class browser cache. | 03 June 2014, 12:15:53 UTC |
| b437395 | Nathaniel Nutter | 02 June 2014, 21:32:36 UTC | sort use statements | 03 June 2014, 02:14:35 UTC |
| 1606150 | Nathaniel Nutter | 02 June 2014, 21:30:11 UTC | preserve setgid bit when chowning Due, I think, to root_squash on NFS the setgid bit is not preserved when chowning even though it would be on a local filesystem. Therefore, this should more correctly model Linux's default behavior. | 03 June 2014, 02:14:34 UTC |
| f036861 | Nathaniel Nutter | 02 June 2014, 21:11:29 UTC | switch to 'mode' | 03 June 2014, 02:14:32 UTC |
| 4a88bd0 | Nathaniel Nutter | 02 June 2014, 21:04:00 UTC | switch to File::stat | 03 June 2014, 02:14:31 UTC |
| 481ff93 | Nathaniel Nutter | 02 June 2014, 21:01:36 UTC | sort use statements | 03 June 2014, 02:14:29 UTC |
| cd33249 | APipe Tester | 02 June 2014, 21:04:39 UTC | updated ur submodule to f9a7c8d | 02 June 2014, 21:04:39 UTC |
| 2c28fbc | APipe Tester | 02 June 2014, 20:12:22 UTC | updated ur submodule to 0b8c6be | 02 June 2014, 20:12:22 UTC |
| 0ddc7b2 | Nathaniel Nutter | 02 June 2014, 20:00:14 UTC | add add/rm method and additional accessors to 'mode' objects | 02 June 2014, 20:01:32 UTC |
| 6cd3cce | Nathaniel Nutter | 02 June 2014, 19:49:21 UTC | check initial and final permissions in case of side effects | 02 June 2014, 20:01:30 UTC |
| 551c0bf | Nathaniel Nutter | 02 June 2014, 19:52:21 UTC | add all_* methods | 02 June 2014, 20:01:28 UTC |
| 1d45175 | Nathaniel Nutter | 02 June 2014, 19:48:55 UTC | add mode, path, and perm instance methods | 02 June 2014, 20:01:26 UTC |
| 23632ac | Nathaniel Nutter | 02 June 2014, 19:28:45 UTC | flip bit/name hash I'm going to add some compound bits so I want to move the bit to the RHS. | 02 June 2014, 20:01:24 UTC |
| 3c7c2db | Nathaniel Nutter | 02 June 2014, 19:21:06 UTC | extract method: set_mode | 02 June 2014, 20:01:22 UTC |
| 0bed757 | Nathaniel Nutter | 02 June 2014, 18:59:10 UTC | add the add/rm methods | 02 June 2014, 20:01:21 UTC |
| 52d6291 | Nathaniel Nutter | 02 June 2014, 18:24:52 UTC | refactor to allow additional methods to be added | 02 June 2014, 20:01:18 UTC |
| d949340 | dmorton | 02 June 2014, 19:14:55 UTC | Use Memoize instead of caching by hand | 02 June 2014, 19:15:14 UTC |
| 91f09eb | Nathaniel Nutter | 30 May 2014, 23:00:20 UTC | add --queue option to unarchive command | 02 June 2014, 19:05:18 UTC |
| 2d5bce6 | Nathaniel Nutter | 02 June 2014, 16:29:12 UTC | refactor file mode tests into new module Refactor Genome::Utility::Test::Stat into Genome::Utility::File::Mode. Implementing as a Test::Builder module limited reuse and defined unnecessary test methods. | 02 June 2014, 16:31:26 UTC |
| 2dc6418 | Nathaniel Nutter | 02 June 2014, 16:26:59 UTC | remove deprecated module | 02 June 2014, 16:31:25 UTC |
| 4147a53 | Nathaniel Nutter | 02 June 2014, 16:26:36 UTC | rename test | 02 June 2014, 16:31:24 UTC |
| 08a21fc | Nathaniel Nutter | 02 June 2014, 16:25:53 UTC | convert test to use 'mode' instead of 'has_bit' | 02 June 2014, 16:31:22 UTC |
| 44299d1 | Nathaniel Nutter | 02 June 2014, 16:11:48 UTC | convert test to use 'mode' instead of 'has_bit' | 02 June 2014, 16:31:21 UTC |
| bed83fb | Nathaniel Nutter | 02 June 2014, 15:59:55 UTC | remove duplicated functionality | 02 June 2014, 16:31:19 UTC |
| 12d5d8c | Nathaniel Nutter | 02 June 2014, 15:59:34 UTC | add Genome::Utility::File::Mode | 02 June 2014, 16:31:18 UTC |
| a5337d1 | Nathaniel Nutter | 02 June 2014, 15:50:37 UTC | fix typo | 02 June 2014, 16:31:16 UTC |
| 5fbda39 | Eddie Belter | 02 June 2014, 16:00:33 UTC | InstData: update lister doc | 02 June 2014, 16:00:33 UTC |
| 2edce28 | Mark Burnett | 02 June 2014, 12:35:27 UTC | G:S:Lock: use 2 hour TTL with Nessy | 02 June 2014, 12:35:27 UTC |
| dc20022 | dmorton | 01 June 2014, 21:21:19 UTC | Fix some missed renames | 01 June 2014, 21:21:19 UTC |
| 135c348 | dmorton | 01 June 2014, 20:32:14 UTC | Fix test and print message about errors. | 01 June 2014, 20:32:14 UTC |
| 3ece69b | dmorton | 01 June 2014, 20:23:26 UTC | Bugfix: Generate more correct header when splitting vep entries | 01 June 2014, 20:24:13 UTC |
| 42b91ed | APipe Tester | 31 May 2014, 12:18:18 UTC | Updated `genome` tab completion. | 31 May 2014, 12:18:18 UTC |
| d276195 | APipe Tester | 31 May 2014, 12:16:40 UTC | Updated class browser cache. | 31 May 2014, 12:16:40 UTC |
| 930559e | Dave Larson | 31 May 2014, 03:31:42 UTC | draft of tool for exome qc metrics for ADSP | 31 May 2014, 03:31:50 UTC |
| c7fcc81 | APipe Tester | 30 May 2014, 23:24:36 UTC | updated ur submodule to 658e160 | 30 May 2014, 23:24:36 UTC |
| 8f500e3 | dmorton | 30 May 2014, 18:16:34 UTC | Bugfix: Vep plugin runtime configuration points to proper locations | 30 May 2014, 20:54:12 UTC |
| 84bfdca | dmorton | 30 May 2014, 16:59:38 UTC | Renamed Genome::Annotation to Genome::VariantReporting | 30 May 2014, 20:54:12 UTC |
| 01d53b2 | APipe Tester | 30 May 2014, 20:52:47 UTC | updated ur submodule to 95b19dc | 30 May 2014, 20:52:47 UTC |
| d7ba99b | APipe Tester | 30 May 2014, 18:53:12 UTC | updated ur submodule to 9211480 | 30 May 2014, 18:53:12 UTC |
| 04ff67e | apregier | 30 May 2014, 18:31:31 UTC | Merge branch 'updated' into gb_master | 30 May 2014, 18:31:31 UTC |
| 9c1a1fe | apregier | 30 May 2014, 18:26:18 UTC | Use default empty hash so we can always set new entries | 30 May 2014, 18:29:44 UTC |
| e083d98 | apregier | 27 May 2014, 20:44:40 UTC | Tumor-only report | 30 May 2014, 18:29:43 UTC |
| d245946 | apregier | 27 May 2014, 19:56:43 UTC | Gmaf interpreter | 30 May 2014, 18:29:43 UTC |
| 6c48f63 | apregier | 27 May 2014, 19:48:45 UTC | Add gmaf filter | 30 May 2014, 18:29:42 UTC |
