| d107953 | Thomas Mooney | 10 December 2012, 15:21:33 UTC | Ignore the index file when diffing--just lists other files. | 10 December 2012, 15:21:33 UTC |
| 4378919 | Scott Smith | 10 December 2012, 04:54:40 UTC | remove check that a model id is an integer so that the code will work with UUID model IDs | 10 December 2012, 04:54:40 UTC |
| 0b51bb2 | Malachi Griffith | 10 December 2012, 00:34:26 UTC | Minor bug fix in clinseq-update analysis | 10 December 2012, 00:34:26 UTC |
| 95feb3e | Scott Smith | 09 December 2012, 08:50:09 UTC | updated weka InlineConfig64 | 09 December 2012, 08:50:09 UTC |
| cea5838 | Scott Smith | 09 December 2012, 08:47:27 UTC | eliminate all warnings during compile of Genome/ modules | 09 December 2012, 08:47:27 UTC |
| b8bde9b | Scott Smith | 09 December 2012, 08:23:11 UTC | made target_region_set_name optional on refalign ...somehow this dodges a check | 09 December 2012, 08:23:11 UTC |
| e11042c | Scott Smith | 09 December 2012, 08:06:43 UTC | ensure fasta chunker does not create directories at compile time | 09 December 2012, 08:06:43 UTC |
| b2b9916 | Scott Smith | 09 December 2012, 08:05:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 December 2012, 08:05:15 UTC |
| 5a19cd4 | Scott Smith | 09 December 2012, 08:04:33 UTC | updated clinseq docs so that Define-docs.t passes | 09 December 2012, 08:04:33 UTC |
| 3b33258 | Malachi Griffith | 09 December 2012, 00:56:08 UTC | Added tool to create simplified VCF from somatic-variation build dir that contains only one column per sample and only hq passing somatic variants | 09 December 2012, 00:56:08 UTC |
| f995271 | Malachi Griffith | 09 December 2012, 00:19:38 UTC | Bug fixes to clin-seq edge cases in dump-igv-xml (undefined sample common name) and cn-view (no cnvhmm segments) | 09 December 2012, 00:19:38 UTC |
| 0beb369 | Scott Smith | 08 December 2012, 23:33:58 UTC | Update how clinseq calls SummarizeTier1SnvSupport. The previous commit failed to pass along all builds, and failed to set a true return value on success. | 08 December 2012, 23:33:58 UTC |
| fb84098 | Scott Smith | 08 December 2012, 21:34:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 08 December 2012, 21:34:07 UTC |
| 08ea277 | Scott Smith | 08 December 2012, 21:33:58 UTC | moved md5sum methods from internal to published portion of Genome::Sys | 08 December 2012, 21:33:58 UTC |
| da29fea | APipe Tester | 08 December 2012, 21:31:56 UTC | updated ur submodule to 27e73cf | 08 December 2012, 21:31:56 UTC |
| ecc8753 | Scott Smith | 08 December 2012, 20:18:54 UTC | fixed error pulling position files | 08 December 2012, 20:18:54 UTC |
| 4e83325 | Scott Smith | 07 December 2012, 23:24:20 UTC | fixed typo in package name for clinseq SummarizeTier1SnvSupport | 07 December 2012, 23:24:20 UTC |
| 30717b9 | Scott Smith | 07 December 2012, 20:17:12 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 07 December 2012, 20:17:12 UTC |
| 5af9868 | Scott Smith | 07 December 2012, 20:17:00 UTC | added clinseq step SummarizeTier1SnvSupport.pm and SummarizeTier1SnvSupport.pm.R | 07 December 2012, 20:17:00 UTC |
| 9b337fe | Nathan Nutter | 07 December 2012, 19:43:04 UTC | add comment about RT #88011 | 07 December 2012, 19:43:04 UTC |
| b1ac3ac | Nathan Nutter | 07 December 2012, 19:41:40 UTC | re-enable | 07 December 2012, 19:41:56 UTC |
| 586ae40 | Malachi Griffith | 07 December 2012, 17:50:15 UTC | Update test results in clin-seq to account for update to update-analysis | 07 December 2012, 17:50:15 UTC |
| 47a767c | Malachi Griffith | 07 December 2012, 16:39:06 UTC | Update clin-seqs definition of a tumor sample to include PIN lesions | 07 December 2012, 16:39:06 UTC |
| c2e65b3 | Malachi Griffith | 07 December 2012, 16:28:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Model/ClinSeq/Command/Main.pm | 07 December 2012, 16:28:48 UTC |
| 33372e9 | Malachi Griffith | 07 December 2012, 16:25:47 UTC | Update to clin-seq main class to handle cases without WGS data | 07 December 2012, 16:25:47 UTC |
| d203490 | Travis Abbott | 07 December 2012, 05:46:08 UTC | add test version of ibwa 0.5 | 07 December 2012, 05:46:08 UTC |
| 949092c | Scott Smith | 07 December 2012, 00:06:05 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 07 December 2012, 00:06:05 UTC |
| a0fbda1 | Scott Smith | 07 December 2012, 00:05:55 UTC | the BAM readcounts for tier 1 SNVs are now done in parallel | 07 December 2012, 00:05:55 UTC |
| 2871cec | APipe Tester | 07 December 2012, 00:05:11 UTC | updated ur submodule to ae12ee1 | 07 December 2012, 00:05:11 UTC |
| 4a0d829 | Thomas Mooney | 06 December 2012, 23:43:34 UTC | Handle contig names with "|" or similar characters by not interpolating input. | 06 December 2012, 23:43:34 UTC |
| 41d34ad | Travis Abbott | 06 December 2012, 22:57:52 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 December 2012, 22:57:52 UTC |
| 56fc35a | Travis Abbott | 06 December 2012, 22:57:11 UTC | use sample names instead of ids in vcf header in gmt vcf create-cross-sample-vcf (indels) | 06 December 2012, 22:57:11 UTC |
| b58fcf7 | Eddie Belter | 06 December 2012, 22:17:01 UTC | Sync: Add sample attr class | 06 December 2012, 22:17:01 UTC |
| bb9e8cb | Thomas Mooney | 06 December 2012, 21:49:38 UTC | First draft of stapling SV assembly validation to end of pipeline. TODO: Bring the pieces up to standards instead of stapling what we've got. | 06 December 2012, 21:49:38 UTC |
| 3447420 | Obi Griffith | 06 December 2012, 21:35:34 UTC | updated archive commands to reflect new tutorial | 06 December 2012, 21:35:34 UTC |
| 80dcdc2 | apregier | 06 December 2012, 21:09:30 UTC | Merge branch 'vep' into gb_master | 06 December 2012, 21:09:30 UTC |
| 5f5fde3 | apregier | 06 December 2012, 15:23:44 UTC | Add Rsid column to the annotation file in somatic variation | 06 December 2012, 20:24:42 UTC |
| 9bfc4db | Travis Abbott | 06 December 2012, 19:50:22 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 December 2012, 19:50:22 UTC |
| 12ec882 | Travis Abbott | 06 December 2012, 19:49:59 UTC | bump vcf version for samtools indel -> vcf fixes | 06 December 2012, 19:49:59 UTC |
| 89a77f1 | Nathan Nutter | 06 December 2012, 19:48:56 UTC | fix incorrect output_files | 06 December 2012, 19:49:03 UTC |
| 55948bd | Travis Abbott | 06 December 2012, 19:46:50 UTC | fix samtools indel -> vcf converter it wasn't handling multiple deletions or calls with an insertion and a deletion properly. | 06 December 2012, 19:46:50 UTC |
| b0e5832 | Nathan Nutter | 06 December 2012, 19:32:39 UTC | whitespace | 06 December 2012, 19:35:05 UTC |
| 4bf70f5 | Nathan Nutter | 06 December 2012, 19:32:27 UTC | fix missing package | 06 December 2012, 19:35:05 UTC |
| 9357359 | Nathan Nutter | 06 December 2012, 19:32:05 UTC | fix missing package | 06 December 2012, 19:35:05 UTC |
| fabf259 | APipe Tester | 06 December 2012, 19:24:32 UTC | updated ur submodule to 1037f9d | 06 December 2012, 19:24:32 UTC |
| b902b1d | Nathan Nutter | 06 December 2012, 19:05:44 UTC | fix typo, early paren | 06 December 2012, 19:05:44 UTC |
| 700841e | Nathan Nutter | 06 December 2012, 19:05:29 UTC | whitespace | 06 December 2012, 19:05:29 UTC |
| 1c54cde | APipe Tester | 06 December 2012, 16:39:10 UTC | Merge remote-tracking branch 'origin/master' | 06 December 2012, 16:39:10 UTC |
| c3b452a | Thomas Mooney | 06 December 2012, 15:50:00 UTC | Report errors mapping workflow inputs. | 06 December 2012, 15:50:00 UTC |
| 2225614 | Nathan Nutter | 06 December 2012, 15:13:17 UTC | Merge "fix bug with unarchiving and moving disk allocaitons" | 06 December 2012, 15:13:17 UTC |
| 2e41682 | Nathan Nutter | 06 December 2012, 03:18:47 UTC | disable | 06 December 2012, 03:18:47 UTC |
| 6fb0472 | Nathan Nutter | 06 December 2012, 01:44:31 UTC | fix for running with UR_DBI_NO_COMMIT - disable UR_DBI_NO_COMMIT for the ur command - grep out undefined rows, etc. | 06 December 2012, 01:44:31 UTC |
| e845110 | Nathan Nutter | 06 December 2012, 00:44:16 UTC | add a couple additional tests - make sure we are in Genome, test failure implied that maybe we aren't - check that ur command exits 0 | 06 December 2012, 00:45:38 UTC |
| 73f8cd1 | Nathan Nutter | 05 December 2012, 23:25:51 UTC | child_exit_code is system exit_cide >> 8 | 05 December 2012, 23:53:43 UTC |
| 2de7575 | Nathan Nutter | 05 December 2012, 21:21:07 UTC | add test to prevent ambiguous property definitions on SoftwareResult subclasses | 05 December 2012, 23:53:42 UTC |
| 5692d36 | Nathan Nutter | 05 December 2012, 21:20:39 UTC | flag more SoftwareResult subclass ambiguous properties | 05 December 2012, 23:53:42 UTC |
| 79c49ab | Scott Smith | 05 December 2012, 21:31:43 UTC | updated to connect the Main result to the output connector for cases in which no steps follow main b/c there is no WGS data. | 05 December 2012, 21:31:43 UTC |
| 981fdc2 | Malachi Griffith | 05 December 2012, 21:15:22 UTC | Various minor updates to druggable-gene importer code | 05 December 2012, 21:15:22 UTC |
| 3db84e6 | Charles Lu | 05 December 2012, 21:08:50 UTC | added documentation | 05 December 2012, 21:08:50 UTC |
| daca5be | Charles Lu | 05 December 2012, 20:53:08 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 December 2012, 20:53:08 UTC |
| 222d195 | Charles Lu | 05 December 2012, 20:53:01 UTC | addeds extra column with GMAF information | 05 December 2012, 20:53:01 UTC |
| 02c4dcd | Kyung Kim | 05 December 2012, 20:33:38 UTC | Updated to make contigs.cmt file in velvet pipeline | 05 December 2012, 20:33:38 UTC |
| deb36bc | Kyung Kim | 05 December 2012, 19:58:59 UTC | Update for new velvet cmt-file tool | 05 December 2012, 19:58:59 UTC |
| 57fcec0 | Kyung Kim | 05 December 2012, 19:58:29 UTC | New velvet tool to create assembly cmt file | 05 December 2012, 19:58:29 UTC |
| 9db39b7 | APipe Tester | 05 December 2012, 19:19:51 UTC | updated jenkins submodule to 9fac041 | 05 December 2012, 19:19:51 UTC |
| 05efa73 | dmorton | 05 December 2012, 18:21:37 UTC | Make 'genome software-result set-test-name' easier to use | 05 December 2012, 18:22:53 UTC |
| 0729939 | APipe Tester | 05 December 2012, 18:11:25 UTC | updated ur submodule to e31ea0e | 05 December 2012, 18:11:25 UTC |
| 87650be | Malachi Griffith | 05 December 2012, 17:25:16 UTC | Added a new druggable-gene importer for TEND: trends in the exploitation of drug targets | 05 December 2012, 17:25:16 UTC |
| 6450f68 | Malachi Griffith | 05 December 2012, 17:24:16 UTC | Update base sub-routines for downloading source in druggable-gene | 05 December 2012, 17:24:16 UTC |
| 804ab90 | Mark Burnett | 05 December 2012, 16:47:22 UTC | fix bug with unarchiving and moving disk allocaitons There were cases where a shadow allocation might not be deleted if an error occurred. This caused subsequent attempts to move or unarchive the same allocation to fail as well. Change-Id: I6e8c20b42d99f05332515b7fb7ac0a5177ee7f99 | 05 December 2012, 16:48:52 UTC |
| 78a0eba | Mark Burnett | 05 December 2012, 15:38:34 UTC | add field Disk::Volume to fix the issues caused by RT #88076 | 05 December 2012, 15:38:34 UTC |
| b6c7e53 | Mark Burnett | 05 December 2012, 15:14:10 UTC | remove SR:Command:FixLookupHashesDV2 We decided to just give the broken results a new test_name. | 05 December 2012, 15:15:58 UTC |
| ade64a3 | Mark Burnett | 05 December 2012, 15:13:22 UTC | make filter_version optional in DV2:R:Vcf:Filter | 05 December 2012, 15:15:58 UTC |
| 821797a | Thomas Mooney | 05 December 2012, 15:07:31 UTC | Also update the list of command names (so tab-completion finds them). | 05 December 2012, 15:07:31 UTC |
| 8ff3626 | Adam Coffman | 04 December 2012, 22:31:24 UTC | Deep copy isn't needed here, and in fact breaks UR's object cache. When the copy goes out of scope, it fires the destroy handler and the original object is cleared too. | 04 December 2012, 22:31:24 UTC |
| 5b237c3 | Gabriel Sanderson | 04 December 2012, 21:54:44 UTC | Merge branch 'master' into gb_master | 04 December 2012, 21:54:44 UTC |
| 6c0d50b | Gabriel Sanderson | 04 December 2012, 21:52:18 UTC | Fixed files ignored by diff | 04 December 2012, 21:54:37 UTC |
| 635d97a | Scott Smith | 04 December 2012, 21:34:50 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 December 2012, 21:34:50 UTC |
| 2e628c0 | Scott Smith | 04 December 2012, 21:34:34 UTC | added a nomenclature filter to Genome::Individual default in/house properties | 04 December 2012, 21:34:34 UTC |
| e05f073 | apregier | 04 December 2012, 21:12:41 UTC | Merge branch 'vep' into gb_master | 04 December 2012, 21:12:41 UTC |
| 0635e15 | apregier | 04 December 2012, 21:10:35 UTC | Add vep cache from gtf capability | 04 December 2012, 21:11:54 UTC |
| d6f4a21 | Scott Smith | 04 December 2012, 21:04:30 UTC | add nomenclature filter to in-house xsample attributes | 04 December 2012, 21:04:30 UTC |
| f0dd4d1 | Eddie Belter | 04 December 2012, 19:53:48 UTC | Misc update: fixes when (not) processing inst data | 04 December 2012, 19:53:59 UTC |
| 077ef46 | dmorton | 04 December 2012, 19:33:52 UTC | Don't die on sanity checks in FixLookupHashesDV2 | 04 December 2012, 19:34:29 UTC |
| e8160d1 | Scott Smith | 04 December 2012, 19:23:37 UTC | ensure checks to common_name go through the default nomenclature ("WUGC" here") | 04 December 2012, 19:23:37 UTC |
| a49edfe | Nathan Nutter | 04 December 2012, 17:34:50 UTC | improve debug message | 04 December 2012, 17:34:50 UTC |
| 912644d | Nathan Nutter | 04 December 2012, 17:34:38 UTC | invert conditional | 04 December 2012, 17:34:38 UTC |
| 896e2c6 | Nathan Nutter | 04 December 2012, 17:33:56 UTC | move vcf_version into the get | 04 December 2012, 17:33:56 UTC |
| 9ee735f | Charles Lu | 04 December 2012, 16:30:55 UTC | fixed a bug so that RSID is matched to the right variant allele | 04 December 2012, 16:30:55 UTC |
| 04673a5 | Thomas Mooney | 04 December 2012, 16:22:58 UTC | Don't include inputs from the helper in type-specific parameters. This fixes model definitions broken by making processing profile an input in 8fb1465afa56aafe2ab6a0baa8152dd4f3f51fd7. | 04 December 2012, 16:22:58 UTC |
| 8c7a264 | Obi Griffith | 04 December 2012, 04:42:01 UTC | added blacklist | 04 December 2012, 04:42:01 UTC |
| cf2d598 | Obi Griffith | 04 December 2012, 04:39:56 UTC | moved Uniprot to Entrez sub to Base.pm | 04 December 2012, 04:39:56 UTC |
| a15387a | Malachi Griffith | 04 December 2012, 03:39:08 UTC | Fix clin-seq update-analysis test and minor update to Main.pm | 04 December 2012, 03:39:08 UTC |
| 5f77a9e | Malachi Griffith | 04 December 2012, 01:12:09 UTC | Cosmetic update to cn-view | 04 December 2012, 01:12:09 UTC |
| 646dd7f | Nathan Nutter | 04 December 2012, 01:10:24 UTC | remove test case for behavior that was removed | 04 December 2012, 01:10:30 UTC |
| db86b3e | Malachi Griffith | 04 December 2012, 00:38:38 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 December 2012, 00:38:38 UTC |
| 6bc1de0 | Nathan Nutter | 04 December 2012, 00:10:24 UTC | remove check that prevents valid, relative link | 04 December 2012, 00:11:39 UTC |
| bef7f0b | Nathan Nutter | 04 December 2012, 00:02:38 UTC | fix typo and hide option | 04 December 2012, 00:11:38 UTC |
| 6bb2dbf | Nathan Nutter | 03 December 2012, 23:52:12 UTC | add blacklisted segments to view | 04 December 2012, 00:11:38 UTC |
| acbf79c | Nathan Nutter | 03 December 2012, 23:18:05 UTC | add ability to blacklist segments - allow segments to be blacklisted by adding one or more blacklisted_segments attributes - make get_segments default to only return non-blacklisted segments but allow overriding with method option | 04 December 2012, 00:11:38 UTC |
