| dab4b1c | Thomas Mooney | 01 October 2012, 13:34:21 UTC | This is what happens when a test diffs against live data. | 01 October 2012, 13:34:21 UTC |
| 3ac8cb9 | APipe Tester | 29 September 2012, 22:44:16 UTC | updated ur submodule to 544ce61 | 29 September 2012, 22:44:16 UTC |
| c9f83bb | Chris Miller | 28 September 2012, 20:53:26 UTC | new tool to query TCGA for UUIDs, add them to a maf, and shift columns accordingly | 28 September 2012, 20:53:38 UTC |
| 20bf0c3 | Ben Oberkfell | 28 September 2012, 20:17:03 UTC | make available version 2.3.2 of varscan | 28 September 2012, 20:17:03 UTC |
| 9774fad | dmorton | 28 September 2012, 17:48:52 UTC | Fix calling gm input show incorrectly. Also put check around terminal size query. | 28 September 2012, 17:48:52 UTC |
| 5e82f85 | dmorton | 28 September 2012, 16:06:27 UTC | Make gmb view show inputs like gm input show | 28 September 2012, 16:07:28 UTC |
| 64f5bf5 | Eddie Belter | 27 September 2012, 22:01:06 UTC | SX: rename input config to params for far, dust and ext cmd base | 27 September 2012, 22:01:28 UTC |
| 5a144f0 | Eddie Belter | 27 September 2012, 21:55:34 UTC | SX: add dust [blast] | 27 September 2012, 22:01:28 UTC |
| 38939cf | Eddie Belter | 27 September 2012, 21:54:41 UTC | SX: return if config does not parse in external cmd base | 27 September 2012, 22:01:27 UTC |
| 6d282e4 | Eddie Belter | 27 September 2012, 21:33:02 UTC | SX: rm test code from external cmd base | 27 September 2012, 22:01:27 UTC |
| 16a1cf8 | Eddie Belter | 27 September 2012, 21:30:10 UTC | SX: add qual file to writer params if exists in external cmd base | 27 September 2012, 22:01:27 UTC |
| e5969c1 | Eddie Belter | 27 September 2012, 20:35:45 UTC | SX: undef input params if writing to cmd input is needed | 27 September 2012, 22:01:26 UTC |
| c338384 | Eddie Belter | 27 September 2012, 20:34:28 UTC | SX: external cmd base returns params for input instead of just files | 27 September 2012, 22:01:26 UTC |
| c7c88fa | Eddie Belter | 27 September 2012, 20:11:50 UTC | SX: Move resolve inputs from FAR to base class ExternalCmdBase | 27 September 2012, 22:01:25 UTC |
| 2917a4e | Eddie Belter | 27 September 2012, 19:26:50 UTC | SX: add type to std in/out reader/writer | 27 September 2012, 22:01:25 UTC |
| 0389402 | Eddie Belter | 27 September 2012, 19:24:46 UTC | SX: add type to sam reader | 27 September 2012, 22:01:25 UTC |
| be9e874 | Eddie Belter | 27 September 2012, 19:23:28 UTC | SX: add type to sff reader | 27 September 2012, 22:01:24 UTC |
| e1318fa | Eddie Belter | 27 September 2012, 19:22:12 UTC | SX: add type to phred reader/writer | 27 September 2012, 22:01:24 UTC |
| 67b6b6f | Eddie Belter | 27 September 2012, 19:19:58 UTC | SX: add type to phred enhanced reader | 27 September 2012, 22:01:24 UTC |
| b23a023 | Eddie Belter | 27 September 2012, 18:52:51 UTC | SX: add type to illumina fastq reader/writer | 27 September 2012, 22:01:23 UTC |
| 3d8793c | Eddie Belter | 27 September 2012, 18:50:44 UTC | SX: add type to fastq reader/writer | 27 September 2012, 22:01:23 UTC |
| f2fc6ce | Eddie Belter | 27 September 2012, 18:48:13 UTC | SX: add type to bam reader | 27 September 2012, 22:01:22 UTC |
| d162442 | Thomas Mooney | 27 September 2012, 21:43:15 UTC | Added libstring-approx-perl to snapshot-deps | 27 September 2012, 21:43:15 UTC |
| d3aec3d | Ben Oberkfell | 27 September 2012, 19:46:33 UTC | change skip file for only new data | 27 September 2012, 19:46:33 UTC |
| 022d7d8 | Ben Oberkfell | 27 September 2012, 19:45:16 UTC | Revert commit to remove accidentally commited change in unrelated file This reverts commit 7c803d735773ad32b57f4d002c857139dea35842. | 27 September 2012, 19:45:16 UTC |
| 7c803d7 | Ben Oberkfell | 27 September 2012, 19:42:23 UTC | change to a new skip file to ensure we sync starting w/ only newly started builds | 27 September 2012, 19:42:32 UTC |
| 83ebe51 | Beifang Niu | 27 September 2012, 19:18:28 UTC | modify code to support VCF format and rearrange help information | 27 September 2012, 19:18:28 UTC |
| 5cb3597 | Travis Abbott | 27 September 2012, 18:50:25 UTC | filter burden summary plots only include things that passed the MAF filter in the burden test | 27 September 2012, 18:51:08 UTC |
| 8deb09a | Feiyu Du | 27 September 2012, 18:17:12 UTC | Remove SOMATIC from Info field | 27 September 2012, 18:17:12 UTC |
| 7ee0ee8 | Charles Lu | 27 September 2012, 18:07:04 UTC | new tool to compare telomere length | 27 September 2012, 18:07:04 UTC |
| c0fecdc | Eddie Belter | 27 September 2012, 18:04:43 UTC | SX: add filters for max Ns and min non Ns | 27 September 2012, 18:04:49 UTC |
| cac9e2f | Christopher C. Harris | 27 September 2012, 17:12:40 UTC | stanky vcfs who need to wash up are now less stanky. fixed DA=1 to be DA=. for new merged vcfs since number of denovo alleleles is no longer capped at one. | 27 September 2012, 17:12:40 UTC |
| 9985f6b | Chris Miller | 27 September 2012, 15:05:45 UTC | adding mm9 as an option | 27 September 2012, 15:05:53 UTC |
| b2844eb | Chris Miller | 27 September 2012, 15:05:12 UTC | added mm9 support | 27 September 2012, 15:05:53 UTC |
| 92663b9 | Cyriac Kandoth | 27 September 2012, 02:20:19 UTC | Support WU format input, and user specified anno DBs | 27 September 2012, 02:20:19 UTC |
| a33a202 | Obi Griffith | 27 September 2012, 01:35:16 UTC | fixed problem with N A Druggable gene category | 27 September 2012, 01:35:16 UTC |
| e45a7dd | Travis Abbott | 26 September 2012, 23:57:42 UTC | make vep reader understand comments | 26 September 2012, 23:58:06 UTC |
| fc2d6f3 | Travis Abbott | 26 September 2012, 23:56:46 UTC | new burden test summary output (phenocorr) We now partition variants into 3 bins in the summary: deleterious and rare deleterious common | 26 September 2012, 23:58:05 UTC |
| 807ff40 | Ben Oberkfell | 26 September 2012, 21:13:57 UTC | Merge branch 'master' of git:/srv/git/genome | 26 September 2012, 21:13:57 UTC |
| d17e483 | Ben Oberkfell | 26 September 2012, 21:13:50 UTC | fix failing test by updating expected status message comparison data | 26 September 2012, 21:13:50 UTC |
| 75fa03f | Anthony Brummett | 26 September 2012, 20:51:34 UTC | Refactor to remove dependancy on Array::Compare Array::Compare has a dependancy on Moose, which we'd rather avoid. The only method it was using was to compare the contents of two lists | 26 September 2012, 20:51:34 UTC |
| 1f301d0 | Jason Walker | 26 September 2012, 20:44:13 UTC | Add a filter for gene biotype to the differential expression in FpkmMatrix | 26 September 2012, 20:45:12 UTC |
| eadbe25 | Eddie Belter | 26 September 2012, 20:43:27 UTC | LIMS/APIPE: rm gsc refs from update genome genotypes | 26 September 2012, 20:43:37 UTC |
| 454e048 | Kyung Kim | 26 September 2012, 20:22:32 UTC | Upate to optionally change taxonomy data base to use | 26 September 2012, 20:22:32 UTC |
| ea5097c | Cyriac Kandoth | 26 September 2012, 20:19:43 UTC | Added option to skip creating a ref-alignment model | 26 September 2012, 20:19:43 UTC |
| a50e43a | Ben Oberkfell | 26 September 2012, 19:56:24 UTC | Merge branch 'master' of git:/srv/git/genome | 26 September 2012, 19:56:24 UTC |
| 02cf5b4 | Ben Oberkfell | 26 September 2012, 19:51:00 UTC | Revert "Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath" This reverts commit 5f0824896210c0b7b6aa9d39e90663d31de16cf2. | 26 September 2012, 19:51:00 UTC |
| 7b07c51 | Ben Oberkfell | 26 September 2012, 19:50:43 UTC | Revert "Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath" This reverts commit aaa0d7b21259c9c3167f3fc90f394d55ecf585ce. | 26 September 2012, 19:50:43 UTC |
| 9d75c06 | Adam Coffman | 26 September 2012, 19:23:19 UTC | add missing theme resource for jquery ui | 26 September 2012, 19:23:19 UTC |
| 29ef6cd | Ben Oberkfell | 26 September 2012, 19:06:34 UTC | Merge branch 'master' of git:/srv/git/genome | 26 September 2012, 19:06:34 UTC |
| cddef7c | Ben Oberkfell | 26 September 2012, 19:06:30 UTC | change bwa resource request to use 2 cpus/8gb RAM per APIPE-2437 | 26 September 2012, 19:06:30 UTC |
| 7b8f213 | apregier | 26 September 2012, 19:05:50 UTC | Merge branch 'allpaths' into gb_master | 26 September 2012, 19:05:50 UTC |
| 2e3375d | apregier | 26 September 2012, 19:04:50 UTC | New version of allpathslg is available in the command | 26 September 2012, 19:05:18 UTC |
| 66e2cbf | APipe Tester | 26 September 2012, 18:54:48 UTC | updated ur submodule to 39ea956 | 26 September 2012, 18:54:48 UTC |
| db894e2 | APipe Tester | 26 September 2012, 18:52:23 UTC | updated workflow submodule to 4895a84 | 26 September 2012, 18:52:23 UTC |
| 9a7ac5d | APipe Tester | 26 September 2012, 18:52:22 UTC | updated ur submodule to 3210d77 | 26 September 2012, 18:52:22 UTC |
| d622e45 | Jim Weible | 26 September 2012, 18:50:58 UTC | Add tool to dump the dgidb database | 26 September 2012, 18:51:04 UTC |
| 8ec9246 | Ben Oberkfell | 26 September 2012, 18:46:47 UTC | Merge branch 'master' of git:/srv/git/genome | 26 September 2012, 18:46:47 UTC |
| 03b0879 | Ben Oberkfell | 26 September 2012, 18:46:36 UTC | update ur submodule | 26 September 2012, 18:46:36 UTC |
| e529772 | Thomas Mooney | 26 September 2012, 18:36:23 UTC | Bring the log-parenting to this workflow as well. | 26 September 2012, 18:36:23 UTC |
| 2a72a51 | Travis Abbott | 26 September 2012, 18:26:04 UTC | remove unused param from BurdenTestSummary maximum_maf is not needed | 26 September 2012, 18:26:47 UTC |
| 0b38ddc | Dan Koboldt | 26 September 2012, 18:24:00 UTC | Merge branch 'master' of git+ssh://git/srv/git/genome | 26 September 2012, 18:24:00 UTC |
| aaa0d7b | Dan Koboldt | 26 September 2012, 18:23:46 UTC | Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath | 26 September 2012, 18:23:46 UTC |
| bcc077c | Travis Abbott | 26 September 2012, 18:18:51 UTC | filter variants used in burden summary by MAF | 26 September 2012, 18:19:30 UTC |
| 5f08248 | Dan Koboldt | 26 September 2012, 18:19:17 UTC | Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath | 26 September 2012, 18:19:17 UTC |
| f4c6018 | Dan Koboldt | 26 September 2012, 15:09:31 UTC | New command-line options to let users define rare and deleterious | 26 September 2012, 15:09:31 UTC |
| a2b1083 | Ben Oberkfell | 26 September 2012, 03:23:10 UTC | add role tables to postgres mapping | 26 September 2012, 03:23:10 UTC |
| c5f2143 | Ben Oberkfell | 26 September 2012, 03:08:09 UTC | remove recursive subclass definition | 26 September 2012, 03:08:09 UTC |
| 41bac10 | Travis Abbott | 26 September 2012, 02:50:49 UTC | BurdenTestSummary now knows about per-alt vcf entries when using VCF info fields, it is important to remain cognizant of the fact that the standard permits certain fields to apply only to certain alternate alleles. | 26 September 2012, 02:52:52 UTC |
| 95dec76 | Travis Abbott | 26 September 2012, 02:19:29 UTC | more header validation in Genome::File::Vcf | 26 September 2012, 02:52:52 UTC |
| 4eefdf8 | Obi Griffith | 26 September 2012, 00:43:05 UTC | Fixed bug in human uniprot check for TTD | 26 September 2012, 00:43:05 UTC |
| 4f6ee32 | Obi Griffith | 26 September 2012, 00:39:24 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 September 2012, 00:39:24 UTC |
| ee898de | Obi Griffith | 26 September 2012, 00:38:55 UTC | Further fixes to importers including removal of non-human TTD and Drugbank proteins, improved base_urls, minor nomenclature changes | 26 September 2012, 00:38:55 UTC |
| a703656 | Travis Abbott | 25 September 2012, 23:17:12 UTC | add burden test summary for PhenoCor | 25 September 2012, 23:17:35 UTC |
| 253c28d | Travis Abbott | 25 September 2012, 22:40:35 UTC | add Genome::File::{Vep,Vcf} Vcf will be replaced by Joinx::Vcf perl bindings soon. | 25 September 2012, 23:17:35 UTC |
| 52ba627 | Malachi Griffith | 25 September 2012, 22:44:36 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 September 2012, 22:44:36 UTC |
| 4b82848 | Malachi Griffith | 25 September 2012, 22:44:18 UTC | Minor bug fixes in automation of clin-seq analysis | 25 September 2012, 22:44:18 UTC |
| b460667 | Beifang Niu | 25 September 2012, 22:08:41 UTC | update help infomation | 25 September 2012, 22:08:41 UTC |
| deb71c6 | APipe Tester | 25 September 2012, 21:48:41 UTC | updated ur submodule to 3210d77 | 25 September 2012, 21:48:41 UTC |
| 693058f | APipe Tester | 25 September 2012, 21:46:02 UTC | updated workflow submodule to 4c33d20 | 25 September 2012, 21:46:02 UTC |
| f0e3421 | APipe Tester | 25 September 2012, 21:46:01 UTC | updated ur submodule to 6ad27f5 | 25 September 2012, 21:46:01 UTC |
| 2c81047 | Ben Oberkfell | 25 September 2012, 21:37:57 UTC | Merge branch 'master' of git:/srv/git/genome | 25 September 2012, 21:37:57 UTC |
| 0c900d2 | Ben Oberkfell | 25 September 2012, 21:37:51 UTC | update ur submodule to remove debug message | 25 September 2012, 21:37:51 UTC |
| 01b8679 | Beifang Niu | 25 September 2012, 21:33:18 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 September 2012, 21:33:18 UTC |
| 8b6510a | Beifang Niu | 25 September 2012, 21:32:36 UTC | First rewrite of cosmic-omim tool by Beifang | 25 September 2012, 21:32:36 UTC |
| 83c287e | Travis Abbott | 25 September 2012, 21:30:04 UTC | look for COUNT= in vep annotation for mutation-diagrams COUNT= will specify the frequency of the allele, which is how many dots to put on the plot. | 25 September 2012, 21:30:47 UTC |
| 7da96e7 | Ben Oberkfell | 25 September 2012, 21:28:36 UTC | Merge branch 'master' of git:/srv/git/genome | 25 September 2012, 21:28:36 UTC |
| e13f8ab | Ben Oberkfell | 25 September 2012, 21:28:24 UTC | update UR submodule with fix | 25 September 2012, 21:28:24 UTC |
| 187d910 | Travis Abbott | 25 September 2012, 21:27:04 UTC | allow querying clinical data for multiple samples at once: attribute_values_for_samples("Phenotype", "s1", "s2", ...) | 25 September 2012, 21:28:21 UTC |
| 287ff17 | Travis Abbott | 25 September 2012, 21:24:33 UTC | do sample verification later so mendelian/none models can succeed sample verification requires clinical data, so models that don't have/need any (trait_type of mendelian/none) were crashing. also added tabix indexing of vcf and per-site vcf report files | 25 September 2012, 21:28:20 UTC |
| 33d9712 | Travis Abbott | 25 September 2012, 21:23:57 UTC | add tabix wrapper | 25 September 2012, 21:28:20 UTC |
| ef17216 | Ben Oberkfell | 25 September 2012, 21:21:50 UTC | update ur submodule | 25 September 2012, 21:21:50 UTC |
| 4160d0e | Eddie Belter | 25 September 2012, 21:15:45 UTC | AQID: Rm DB::singles | 25 September 2012, 21:15:45 UTC |
| 7f08535 | Eddie Belter | 25 September 2012, 21:01:41 UTC | AQID: rm comment | 25 September 2012, 21:01:41 UTC |
| acf3e3c | Eddie Belter | 25 September 2012, 20:59:51 UTC | Rm AQID refs from white list | 25 September 2012, 20:59:51 UTC |
| c21e53d | Eddie Belter | 25 September 2012, 20:57:54 UTC | Mistakenly added a temporary script [p.pl] | 25 September 2012, 20:58:21 UTC |
| 1148a7c | Eddie Belter | 25 September 2012, 20:56:18 UTC | Sync: add pipeline prop to setup project view; AQID: use sync setup project view to get pipeline instead of gsc work order | 25 September 2012, 20:56:24 UTC |
| 33a44ad | APipe Tester | 25 September 2012, 20:35:33 UTC | updated workflow submodule to 547bb03 | 25 September 2012, 20:35:33 UTC |
| c22ae13 | Nathan Dees | 25 September 2012, 19:14:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 September 2012, 19:14:07 UTC |
| 13d6f1f | Nathan Dees | 25 September 2012, 19:14:00 UTC | removed default pointing to build 36 reference - a dangerous practice | 25 September 2012, 19:14:00 UTC |
