| 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 |
| 7de3beb | Thomas Mooney | 25 September 2012, 18:18:40 UTC | Point to the new BER location | 25 September 2012, 18:18:40 UTC |
| cbf9cf2 | APipe Tester | 25 September 2012, 17:56:57 UTC | updated ur submodule to 6ad27f5 | 25 September 2012, 17:56:57 UTC |
| fa3cde1 | Thomas Mooney | 25 September 2012, 17:54:40 UTC | Queue the model update instead of adding inline. | 25 September 2012, 17:54:40 UTC |
| 7e66e6c | Jason Walker | 25 September 2012, 16:21:54 UTC | Add an option to remove MT genes from TranscriptomeCoverage in the RnaSeq pipeline | 25 September 2012, 16:22:18 UTC |
| 613345e | Jason Walker | 25 September 2012, 15:07:05 UTC | Add differential expression to the FpkmMatrix using quantile normalization and Log2Diff of Mean/Median values. | 25 September 2012, 16:22:17 UTC |
| 59b8b2e | Thomas Mooney | 25 September 2012, 16:05:46 UTC | Requeue the model in the search queue on build success. | 25 September 2012, 16:05:46 UTC |
| 9eb3577 | Chris Miller | 25 September 2012, 15:05:23 UTC | added undo splits option, made default | 25 September 2012, 15:05:32 UTC |
| eb2d0b0 | Chris Miller | 25 September 2012, 15:02:19 UTC | now correctly handles maf header of either case | 25 September 2012, 15:05:32 UTC |
| 40de07d | Nathaniel Nutter | 14 September 2012, 14:05:41 UTC | break Music.t into many tests so that it is more easily parallelizable | 25 September 2012, 14:36:24 UTC |
| 352e01b | Thomas Mooney | 25 September 2012, 14:33:43 UTC | ...Update test data again... | 25 September 2012, 14:33:43 UTC |
| 75bc0c4 | Obi Griffith | 25 September 2012, 13:32:20 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 September 2012, 13:32:20 UTC |
| f52f24a | Obi Griffith | 25 September 2012, 13:31:33 UTC | changed way missing values are dealt with in importers | 25 September 2012, 13:31:33 UTC |
| 3e93608 | Thomas Mooney | 24 September 2012, 20:33:48 UTC | Reallocation failure shouldn't fail the DV2 step. | 24 September 2012, 20:33:48 UTC |
| 9e7c803 | Obi Griffith | 24 September 2012, 19:41:57 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 September 2012, 19:41:57 UTC |
| 6e95207 | Obi Griffith | 24 September 2012, 19:41:45 UTC | various minor fixes to importers | 24 September 2012, 19:41:45 UTC |
| b73352a | Thomas Mooney | 24 September 2012, 19:35:14 UTC | Update whitelist line. | 24 September 2012, 19:35:14 UTC |
| cddc0f0 | Feiyu Du | 24 September 2012, 19:22:59 UTC | CHANGELOG more TCGA-compliance vcf format change, add TCGA format output of snv and indel to strelka tool, add fix to Varscan Somatic snv vcf, fix all broken unit tests | 24 September 2012, 19:22:59 UTC |
| 992f0a0 | Kyung Kim | 24 September 2012, 15:45:57 UTC | clean up | 24 September 2012, 15:45:57 UTC |
| 4e157d9 | Jim Weible | 24 September 2012, 15:18:16 UTC | update the base_url for pharmgkb | 24 September 2012, 15:18:21 UTC |
| 4974095 | Kyung Kim | 24 September 2012, 15:06:47 UTC | Made databases to be used command option | 24 September 2012, 15:06:47 UTC |
| ac5a459 | Jim Weible | 24 September 2012, 14:38:34 UTC | fix the nomenclautre for gene grouping so that it actually works | 24 September 2012, 14:38:34 UTC |
| 15a8b00 | Jim Weible | 24 September 2012, 13:55:51 UTC | update gene group generator to handle new nomenclature | 24 September 2012, 13:55:51 UTC |
| a043f89 | Malachi Griffith | 24 September 2012, 03:59:08 UTC | Fixed clin-seq test cases that were failing do to database updates that changed the results of some queries | 24 September 2012, 03:59:08 UTC |
| fff337f | Malachi Griffith | 24 September 2012, 03:47:20 UTC | Fix minor bug in clinseq update-analysis that resulted in miss counting of WGS and RNAseq data | 24 September 2012, 03:47:20 UTC |
| 9958ef5 | Malachi Griffith | 23 September 2012, 23:45:08 UTC | Cosmetic updates to warnings, added additional possible designations for tumor samples, etc. to clinseq update-analysis | 23 September 2012, 23:45:08 UTC |
| ed4ea51 | Malachi Griffith | 23 September 2012, 22:41:03 UTC | Improve recognition of non-normal sample types when checking or creating clinseq input models | 23 September 2012, 22:41:03 UTC |
| 47b791a | dmorton | 23 September 2012, 04:50:58 UTC | Remove non-working feature in DV2 Dispatcher And the code that was "testing" it in the PhenotypeCorrelation unittest. | 23 September 2012, 04:55:30 UTC |
| 8ad922e | Kyung Kim | 21 September 2012, 22:03:29 UTC | Update to change comments to log file | 21 September 2012, 22:03:29 UTC |
| dfdf812 | Kyung Kim | 21 September 2012, 22:02:09 UTC | Update to change comments to log file | 21 September 2012, 22:02:09 UTC |
| 2450d91 | Kyung Kim | 21 September 2012, 21:59:59 UTC | Update to change comments to log file | 21 September 2012, 21:59:59 UTC |
| 029b9ef | dmorton | 21 September 2012, 20:58:55 UTC | CreateCrossSampleVcf takes FeatureList Previously used a roi bed file directly and this sometimes needed to be converted to a new reference sequence. That functionality is present in the FeatureList so we require a FeatureList instead. | 21 September 2012, 21:02:49 UTC |
| 4852c21 | dmorton | 21 September 2012, 20:57:33 UTC | Improve caching in FeatureList Previously the caching would blindly accept it's cached version, now it will check that the cached result exists before trying to use it. | 21 September 2012, 21:02:49 UTC |
| 8d542f0 | APipe Tester | 21 September 2012, 20:51:58 UTC | updated ur submodule to 89878ad | 21 September 2012, 20:51:58 UTC |
| fd473cc | Justin Lolofie | 21 September 2012, 20:05:39 UTC | seperate search results for clinseq/convergence | 21 September 2012, 20:05:39 UTC |
