| 5b194f9 | APipe Tester | 14 November 2012, 21:32:50 UTC | updated jenkins submodule to 6dbe3a7 | 14 November 2012, 21:32:50 UTC |
| c107b96 | Thomas Mooney | 14 November 2012, 20:48:37 UTC | Remove old error mailing--this caused errors since App::Mail isn't imported. The result was that exit() wasn't reached and both sides of the fork continued when the command had been eval{}ed (such as under workflow. | 14 November 2012, 20:48:37 UTC |
| 71c03b2 | Scott Smith | 14 November 2012, 20:18:31 UTC | fix warning message in dbpath in Genome::Sys | 14 November 2012, 20:18:31 UTC |
| 2c5671f | Scott Smith | 14 November 2012, 20:16:11 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 November 2012, 20:16:11 UTC |
| c2ceab4 | Nathan Nutter | 14 November 2012, 16:52:08 UTC | updated ur submodule (includes Tony's Oracle 11 fix) Change-Id: I1d7041c8d81a8a42ebde08465586dac2c59685df | 14 November 2012, 16:53:01 UTC |
| f492fb2 | Jason Walker | 14 November 2012, 14:48:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 November 2012, 14:48:03 UTC |
| 20db422 | Jason Walker | 14 November 2012, 14:47:00 UTC | Revert changes that used the python module from chimerascan to convert GTF to genePred format. The CDS start stop is not working with Picard CollectRnaSeqMetrics | 14 November 2012, 14:47:00 UTC |
| 3252ce8 | Scott Smith | 14 November 2012, 02:31:05 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 November 2012, 02:31:05 UTC |
| 8a8501f | Obi Griffith | 14 November 2012, 01:39:49 UTC | merge branch 'master' of ssh://git/srv/git/genome | 14 November 2012, 01:39:49 UTC |
| 6a32657 | Obi Griffith | 14 November 2012, 01:39:28 UTC | refactored CnView tool | 14 November 2012, 01:39:28 UTC |
| f7f2f81 | Gabriel Sanderson | 14 November 2012, 00:17:58 UTC | Merge branch 'tcga' into gb_master | 14 November 2012, 00:17:58 UTC |
| e5f441a | Gabriel Sanderson | 14 November 2012, 00:17:47 UTC | Fixed package_file_for_tcga | 14 November 2012, 00:17:47 UTC |
| f9f78ff | Gabriel Sanderson | 13 November 2012, 23:35:32 UTC | Merge branch 'tcga' into gb_master | 13 November 2012, 23:35:32 UTC |
| 1c877c3 | Gabriel Sanderson | 13 November 2012, 23:34:46 UTC | yep | 13 November 2012, 23:34:46 UTC |
| 3195523 | Gabriel Sanderson | 08 November 2012, 21:04:11 UTC | CHANGELOG: Add gmt vcf tcga-sanitize for TCGA-ifying vcfs Also added some methods to Genome Utility VCF, from DV2 vcf filters. Refactor of those modules is forthcoming. | 13 November 2012, 23:31:52 UTC |
| 84daaa6 | Obi Griffith | 13 November 2012, 22:59:30 UTC | misc clinical trials stuff | 13 November 2012, 22:59:30 UTC |
| 7c2789f | Cyriac Kandoth | 13 November 2012, 21:51:11 UTC | Fixed incorrect check for #muts > #covd_bps for a gene | 13 November 2012, 21:51:11 UTC |
| 1703f5c | Scott Smith | 13 November 2012, 21:39:38 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 November 2012, 21:39:38 UTC |
| 12fced1 | Beifang Niu | 13 November 2012, 21:18:46 UTC | change some code for Cosmic | 13 November 2012, 21:39:22 UTC |
| 108cded | Beifang Niu | 13 November 2012, 21:09:42 UTC | change some code | 13 November 2012, 21:39:21 UTC |
| c1c4a55 | Beifang Niu | 13 November 2012, 20:59:09 UTC | code improve | 13 November 2012, 21:39:21 UTC |
| c5c9fd1 | Beifang Niu | 13 November 2012, 20:58:56 UTC | code improve | 13 November 2012, 21:39:20 UTC |
| c49ab4c | Malachi Griffith | 13 November 2012, 19:50:37 UTC | Various updates to clin-seq output, added mutation-diagram creation to main pipeline | 13 November 2012, 21:39:20 UTC |
| 2a2ee03 | apregier | 13 November 2012, 18:38:25 UTC | Only attempt lookup_conservation_score once. If it fails, warn and stop trying for remaining variants | 13 November 2012, 21:39:19 UTC |
| 8e0beaf | Beifang Niu | 13 November 2012, 21:18:46 UTC | change some code for Cosmic | 13 November 2012, 21:18:46 UTC |
| ea88ad9 | Beifang Niu | 13 November 2012, 21:09:42 UTC | change some code | 13 November 2012, 21:09:42 UTC |
| ba6d50a | Beifang Niu | 13 November 2012, 21:05:27 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 November 2012, 21:05:27 UTC |
| 4f65f45 | Beifang Niu | 13 November 2012, 20:59:09 UTC | code improve | 13 November 2012, 20:59:09 UTC |
| 0e15b81 | Beifang Niu | 13 November 2012, 20:58:56 UTC | code improve | 13 November 2012, 20:58:56 UTC |
| 48e62db | Malachi Griffith | 13 November 2012, 19:50:37 UTC | Various updates to clin-seq output, added mutation-diagram creation to main pipeline | 13 November 2012, 19:50:37 UTC |
| 6323788 | apregier | 13 November 2012, 18:39:16 UTC | Merge branch 'fix' into gb_master | 13 November 2012, 18:39:16 UTC |
| 746ebf5 | apregier | 13 November 2012, 18:38:25 UTC | Only attempt lookup_conservation_score once. If it fails, warn and stop trying for remaining variants | 13 November 2012, 18:38:51 UTC |
| 2335512 | Travis Abbott | 12 November 2012, 23:33:22 UTC | add optional --file-suffix option to gmt graph mutation-diagram | 12 November 2012, 23:33:22 UTC |
| 52097fe | apregier | 12 November 2012, 22:51:42 UTC | Merge branch 'fix' into gb_master | 12 November 2012, 22:51:42 UTC |
| 300839c | apregier | 12 November 2012, 22:51:09 UTC | Ignore some files for build diffs in somatic variation. This is necessary because of the strelka output files. We also now grep out some lines from all .hq files such as fileDate,cmdline, and startTime | 12 November 2012, 22:51:25 UTC |
| 55164f7 | APipe Tester | 12 November 2012, 20:48:36 UTC | Merge remote-tracking branch 'origin/master' | 12 November 2012, 20:48:36 UTC |
| 1db4ebf | apregier | 12 November 2012, 19:59:12 UTC | Merge branch 'fix' into gb_master | 12 November 2012, 19:59:12 UTC |
| c1a3c59 | apregier | 12 November 2012, 19:55:29 UTC | Update test with new expected outputs | 12 November 2012, 19:55:29 UTC |
| 59d056b | Eddie Belter | 12 November 2012, 19:25:05 UTC | Solexa: rm original fastqs after SX trimming | 12 November 2012, 19:25:12 UTC |
| 581e653 | Thomas Mooney | 12 November 2012, 19:22:18 UTC | Correct locking when software result has an object as input or param. Previously the inputs and params were simply concatenated together; however in the case of objects this would use their memory address, which is unsuitable for a lock across processes. The locks generated should be the same for results without objects--only locks that currently don't work are changing! | 12 November 2012, 19:22:18 UTC |
| d01f505 | Dave Larson | 12 November 2012, 18:47:44 UTC | add change to allow overflow passthrough to work | 12 November 2012, 18:47:44 UTC |
| 929d7aa | Dave Larson | 12 November 2012, 18:27:13 UTC | test making backbone overflow:visible part of style | 12 November 2012, 18:27:13 UTC |
| 8dd99f6 | Dave Larson | 31 October 2012, 14:42:42 UTC | switched to counting non-reference alleles. Made exclusion of non-biallelic loci optional | 12 November 2012, 18:23:08 UTC |
| 41c979b | Malachi Griffith | 12 November 2012, 18:05:32 UTC | Added clinseq module to automatically generate mutation-diagram plots for case and cosmic variants | 12 November 2012, 18:05:32 UTC |
| 23ae45a | Malachi Griffith | 12 November 2012, 18:04:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 November 2012, 18:04:17 UTC |
| fa1c4a4 | Mark Burnett | 12 November 2012, 17:17:31 UTC | Merge changes I4e776ad9,Ie0a9d9eb,Id002688b,I0c16bbcf,I4f22ddbb * changes: use set operation use UR::Object::Set's server-side aggregate logic add timer instrumentation refactor allocated_kb body into sub improve reliability of the allocate with move test | 12 November 2012, 17:17:31 UTC |
| 6ac0b89 | Mark Burnett | 12 November 2012, 17:11:58 UTC | Merge "fix typo" | 12 November 2012, 17:11:58 UTC |
| b57e427 | Nathan Nutter | 09 November 2012, 21:36:27 UTC | Merge "change paired end inferrence to be less aggressive" | 09 November 2012, 21:36:27 UTC |
| d8cca35 | Malachi Griffith | 09 November 2012, 18:14:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 November 2012, 18:14:03 UTC |
| d754ca1 | Feiyu Du | 09 November 2012, 17:27:59 UTC | change the description of format FT to be TCGA-compliant | 09 November 2012, 17:27:59 UTC |
| c114b71 | Nathan Nutter | 08 November 2012, 22:50:04 UTC | change paired end inferrence to be less aggressive - If >= 90% paired end then run as paired end. - Else If <= 10% paired end then run as single end. - Else die. Change-Id: I755ce8659ee3d4ac1c2b339881e551289241f013 | 08 November 2012, 22:57:07 UTC |
| ac8bfbf | Thomas Mooney | 08 November 2012, 22:17:31 UTC | Add a few files containing paths to the list ignored by the build diff. | 08 November 2012, 22:17:31 UTC |
| df967e5 | Nathan Nutter | 08 November 2012, 22:05:29 UTC | use set operation This is still pretty hairy since we have to prevent UR from caching aggregate value. Change-Id: I4e776ad91612a34b379c168143d1765cf507eca5 | 08 November 2012, 22:14:25 UTC |
| 6b21c7b | Nathan Nutter | 08 November 2012, 21:52:07 UTC | use UR::Object::Set's server-side aggregate logic Change-Id: Ie0a9d9eb63b4508b443c7a405f2c4a462b159c1d | 08 November 2012, 22:14:24 UTC |
| ad0ee65 | Nathan Nutter | 08 November 2012, 21:23:08 UTC | add timer instrumentation Change-Id: Id002688b67d5e6e5f84988bb6572b5babb6856d8 | 08 November 2012, 22:14:23 UTC |
| c4b35dc | Nathan Nutter | 08 November 2012, 21:09:27 UTC | refactor allocated_kb body into sub Change-Id: I0c16bbcf5720a9b4f712b4f5e1a4f4892d89e3f3 | 08 November 2012, 22:14:22 UTC |
| 1a6603e | Nathan Nutter | 08 November 2012, 22:14:05 UTC | improve reliability of the allocate with move test Change-Id: I4f22ddbbd84d8c9973c6ef46783ac681a17469aa | 08 November 2012, 22:14:22 UTC |
| f315b72 | Anthony Brummett | 08 November 2012, 21:22:56 UTC | value_class_name was listed as an ID property, but not as a primary key column, so deletions were not working | 08 November 2012, 21:53:58 UTC |
| 2e763a4 | Nathan Nutter | 08 November 2012, 21:05:38 UTC | fix typo Change-Id: I5e4c644b5f05cc3bd8b74dc8e83e6b6b8fdf913c | 08 November 2012, 21:05:38 UTC |
| 7fc1648 | Adam Coffman | 08 November 2012, 20:52:08 UTC | Merge "Refactored logic into helper function Change-Id: I6bc17bc75d298c7aefa9e0ad94808c244480eefa" | 08 November 2012, 20:52:08 UTC |
| 9b9dfbc | APipe Tester | 08 November 2012, 20:38:03 UTC | Merge remote-tracking branch 'origin/master' | 08 November 2012, 20:38:03 UTC |
| d563ebd | Mark Burnett | 08 November 2012, 20:02:17 UTC | Merge "remove "random" call to volume" | 08 November 2012, 20:02:17 UTC |
| 67d172f | Mark Burnett | 08 November 2012, 20:00:02 UTC | Merge "only reload when committing" | 08 November 2012, 20:00:02 UTC |
| 8b7b512 | dmorton | 08 November 2012, 19:52:32 UTC | Refactored logic into helper function Change-Id: I6bc17bc75d298c7aefa9e0ad94808c244480eefa removed unused lib and whitespace Change-Id: Iec797bf4e4487dc03a95ec70c5e8442a5279aa2b Add --bowtie-version specification to chimerascan params You can now do something like: fusion_detection_strategy: 'chimerascan -v 0.4.5 [-p 2 --bowtie-version=0.12.7]' and only '-p 2' will be passed on to chimerascan and we take care of telling chimerascan what version of bowtie to use. You must supply a bowtie-version, and it currently must be of major version 0. Change-Id: I179271018de084d8a8f9caa713094a3347a39678 | 08 November 2012, 19:52:32 UTC |
| 940c28c | Cyriac Kandoth | 08 November 2012, 19:45:46 UTC | Added a hash to properly classify biotypes into ncRNA and pseudogenes. | 08 November 2012, 19:45:46 UTC |
| 7abd168 | Adam Coffman | 08 November 2012, 19:16:34 UTC | Merge "Fix how fusion_detection_strategy is parsed" | 08 November 2012, 19:16:34 UTC |
| 42f6365 | Malachi Griffith | 08 November 2012, 17:38:21 UTC | Minor update to clinseq update-analysis | 08 November 2012, 17:38:21 UTC |
| 8acb73b | Travis Abbott | 08 November 2012, 16:47:23 UTC | Fix dbsnp info field calculation | 08 November 2012, 16:48:13 UTC |
| b925f6d | dmorton | 08 November 2012, 16:15:35 UTC | Fix how fusion_detection_strategy is parsed Didn't take into account spaces in detector_params. Build shouldn't reference model explicitly. Change-Id: I6d685df2a3a38ce9efe1fa4b6da55d20af6a8ec7 | 08 November 2012, 16:33:57 UTC |
| 4148944 | Thomas Mooney | 08 November 2012, 16:12:57 UTC | Change somatic-variation PP to the Oct 2012 defaults (RT#87515) | 08 November 2012, 16:12:57 UTC |
| a2274bf | APipe Tester | 08 November 2012, 16:07:08 UTC | updated ur submodule to 1ab73d5 | 08 November 2012, 16:07:08 UTC |
| f3e0a82 | Thomas Mooney | 08 November 2012, 14:08:38 UTC | Testing with live data continues to make us cry. Update expected results. | 08 November 2012, 14:08:38 UTC |
| fe86aeb | Thomas Mooney | 08 November 2012, 03:31:10 UTC | Only annotate if we have something to annotate. | 08 November 2012, 03:31:10 UTC |
| 23359bc | Eddie Belter | 08 November 2012, 00:57:05 UTC | DV2 Breakdancer: add fastq validation when running -d | 08 November 2012, 00:57:41 UTC |
| 06da733 | Eddie Belter | 08 November 2012, 00:56:36 UTC | SX: add validate method to seq reader | 08 November 2012, 00:57:41 UTC |
| 45609aa | Scott Smith | 06 November 2012, 21:35:42 UTC | md5 fastqs | 08 November 2012, 00:57:40 UTC |
| 85c8dcf | Scott Smith | 06 November 2012, 16:55:59 UTC | remove hard-coded nomenclature in instrument data attribute constructor | 08 November 2012, 00:57:40 UTC |
| 43d10c9 | Scott Smith | 06 November 2012, 16:50:10 UTC | made the default nomenclature for instrument data come from an environment config not a hard-coded value | 08 November 2012, 00:57:40 UTC |
| 56ff4df | Eddie Belter | 08 November 2012, 00:39:54 UTC | MC16s 454 test: lower the number of levels when checking classifications b/c it is not deterministic | 08 November 2012, 00:39:54 UTC |
| 5cc44d4 | Chris Miller | 07 November 2012, 22:53:13 UTC | checking for the presence of the variable before trying to split it - a novel idea | 07 November 2012, 22:53:47 UTC |
| 7501659 | Thomas Mooney | 07 November 2012, 22:35:54 UTC | Examine one level deeper (i.e. via the merged results) for the build | 07 November 2012, 22:35:54 UTC |
| 6da4897 | Travis Abbott | 07 November 2012, 22:30:27 UTC | add missing : in phenotype correlation dbsnp info fields | 07 November 2012, 22:30:27 UTC |
| 290654f | Travis Abbott | 07 November 2012, 21:03:06 UTC | update dbsnp info fields in phenotypecorrelation in dbsnp137+, the CLN field has become PM. As an intermediate step on the path to having an annotation_strategy as part of the processing profile, there is now a method that returns the proper info fields for a given dbsnp version. | 07 November 2012, 21:04:31 UTC |
| c2309aa | Nathan Nutter | 06 November 2012, 22:02:19 UTC | remove "random" call to volume Change-Id: Ib02ec6b91ccd50b6d4bd4862d0345b47aca8d085 | 07 November 2012, 20:21:11 UTC |
| 89bb1d3 | Nathan Nutter | 07 November 2012, 20:08:03 UTC | only reload when committing Change-Id: I4ae0489f51ec6e8ba086c44d3705ad4d3e6a0868 | 07 November 2012, 20:21:02 UTC |
| e2200c1 | Jason Walker | 07 November 2012, 19:39:49 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 07 November 2012, 19:39:49 UTC |
| 406d984 | Jason Walker | 07 November 2012, 19:39:39 UTC | Remove the Jim Kent binary for converting gtfToGenePred in favor of the chimerascan tool gtf_to_genepred.py | 07 November 2012, 19:39:39 UTC |
| 608ecf3 | APipe Tester | 07 November 2012, 19:10:10 UTC | Merge remote-tracking branch 'origin/master' | 07 November 2012, 19:10:10 UTC |
| a2590ee | Thomas Mooney | 07 November 2012, 18:20:32 UTC | Skip tiering if there were no qualifying variants. | 07 November 2012, 18:20:32 UTC |
| 19e13b6 | Nathan Nutter | 07 November 2012, 17:00:48 UTC | Merge "Fix how we find Chimerascan for a given version." | 07 November 2012, 17:00:48 UTC |
| f362bfe | Thomas Mooney | 07 November 2012, 15:33:16 UTC | Make annotation build required on validation builds. | 07 November 2012, 15:33:16 UTC |
| c16f0cb | Gabriel Sanderson | 06 November 2012, 23:27:22 UTC | Merge branch 'master' into gb_master | 06 November 2012, 23:27:22 UTC |
| 4de72d5 | Gabriel Sanderson | 06 November 2012, 23:27:06 UTC | If all vcf files are not present, inform the user which builds did and did not have them. | 06 November 2012, 23:27:06 UTC |
| 430aa53 | dmorton | 05 November 2012, 22:44:43 UTC | Fix how we find Chimerascan for a given version. It didn't used to try to find the installation in the typical debian install location. Change-Id: I8ef0f9f0ddc02ef4cb3c01fbacea3ae795b1e8d4 | 06 November 2012, 22:47:59 UTC |
| 9ac0fd8 | Nathaniel Nutter | 06 November 2012, 21:16:55 UTC | work around weird openmpi behavior | 06 November 2012, 21:17:21 UTC |
| 5f80fc0 | apregier | 06 November 2012, 20:54:16 UTC | Merge branch 'fireteam2' into gb_master | 06 November 2012, 20:54:16 UTC |
| 6fb8260 | apregier | 06 November 2012, 20:53:52 UTC | Use Ensembl BiotypeMapper API | 06 November 2012, 20:53:52 UTC |
| a98c349 | dmorton | 06 November 2012, 20:08:41 UTC | Fix how get_vcf_header was being used. | 06 November 2012, 20:08:41 UTC |
| 8030ff5 | dmorton | 06 November 2012, 20:06:57 UTC | Fix mistake in Utility/Vcf get_vcf_header had stupid parameter handling mistake. Added test for get_vcf_header. | 06 November 2012, 20:06:57 UTC |
| 8fbf3d5 | Nathaniel Nutter | 06 November 2012, 16:13:45 UTC | fix invalid call to mkpath mkpath was probably meant to be File::Path's make_path but even more so it should be Genome::Sys->create_directory | 06 November 2012, 16:43:16 UTC |
