| 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 |
| 8178ea7 | Justin Lolofie | 21 September 2012, 19:09:17 UTC | link to alloc page from build status page | 21 September 2012, 19:09:17 UTC |
| d49f555 | Jason Walker | 21 September 2012, 14:35:01 UTC | Add significant gene heatmap | 21 September 2012, 14:35:01 UTC |
| 5ec75cc | Malachi Griffith | 21 September 2012, 02:44:57 UTC | Finished first complete version of clinseq update-analysis | 21 September 2012, 02:44:57 UTC |
| 2b8e648 | Justin Lolofie | 20 September 2012, 22:09:48 UTC | page to display allocations for a build | 20 September 2012, 22:09:48 UTC |
| 9781e8c | Dave Larson | 20 September 2012, 21:59:23 UTC | new version of pairoscope for deploy | 20 September 2012, 21:59:29 UTC |
| bcf262e | Dave Larson | 20 September 2012, 21:58:56 UTC | bugfix version release | 20 September 2012, 21:59:29 UTC |
| 16e652b | apregier | 20 September 2012, 20:45:00 UTC | Merge branch 'updated' into gb_master | 20 September 2012, 20:45:00 UTC |
| 442ca75 | apregier | 20 September 2012, 20:44:18 UTC | prepare_output_directory after staging directory is created and filled | 20 September 2012, 20:44:18 UTC |
| a8ec08b | apregier | 20 September 2012, 19:05:54 UTC | Merge branch 'updated' into gb_master | 20 September 2012, 19:05:54 UTC |
| f6f0279 | apregier | 20 September 2012, 19:03:54 UTC | Don't set previously_discovered_variations input | 20 September 2012, 19:05:33 UTC |
| eb53dd4 | APipe Tester | 20 September 2012, 18:23:28 UTC | updated ur submodule to 158f419 | 20 September 2012, 18:23:28 UTC |
| 21d365a | Eddie Belter | 20 September 2012, 17:37:45 UTC | AQID: is_mc16s justs looks for 16s in work order pipeline | 20 September 2012, 17:37:45 UTC |
| afbd421 | Jason Walker | 20 September 2012, 17:09:29 UTC | Remove path to acoffman tophat2.0.4 | 20 September 2012, 17:09:29 UTC |
| 96bf5b3 | Jason Walker | 20 September 2012, 17:07:37 UTC | Remove jwalker path for cufflinks2.0.2 | 20 September 2012, 17:07:37 UTC |
| ad29987 | Dave Larson | 20 September 2012, 16:08:41 UTC | fix use statement for Genome::Utility::Vcf | 20 September 2012, 16:08:47 UTC |
| da4c7a0 | dmorton | 20 September 2012, 15:58:25 UTC | Ensure converted roi bed is put on network disk instead of on tmp where it cannot be accessed by the other blades. | 20 September 2012, 15:59:09 UTC |
| 26f917a | apregier | 20 September 2012, 15:54:24 UTC | Merge branch 'updated' into gb_master | 20 September 2012, 15:54:24 UTC |
| 0dc4b39 | apregier | 20 September 2012, 15:53:50 UTC | Revert "Don't set previously_discovered_variations input" Oops This reverts commit 80e9da7301629b44b90e090e8e75a98cd9d83b9a. | 20 September 2012, 15:53:50 UTC |
| 60db36e | apregier | 20 September 2012, 15:05:34 UTC | Merge branch 'updated' into gb_master | 20 September 2012, 15:05:34 UTC |
| 80e9da7 | apregier | 20 September 2012, 15:03:31 UTC | Don't set previously_discovered_variations input | 20 September 2012, 15:03:31 UTC |
| 8cfa505 | Eddie Belter | 19 September 2012, 23:21:47 UTC | CHANGELOG: AQID - NO MORE QIDFGM REFS! | 19 September 2012, 23:21:54 UTC |
| 2d664d0 | Jason Walker | 19 September 2012, 21:04:20 UTC | Define the merged transcript gtf file path for cuffmerge. | 19 September 2012, 21:04:20 UTC |
| 64a0f17 | Jason Walker | 19 September 2012, 20:57:38 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 September 2012, 20:57:38 UTC |
| ff95a80 | Jason Walker | 19 September 2012, 20:57:20 UTC | Add cuffmerge functionality to the differential-expression pipeline for RnaSeq. Also move a few command classes to avoid having subclassig/subdirectories. | 19 September 2012, 20:57:20 UTC |
| b44eae7 | Eddie Belter | 19 September 2012, 20:47:25 UTC | Sync: allow syncing of 454 w/o SFF file. Problems (has reads, but no SFF) should be caught in POIDFA | 19 September 2012, 20:47:25 UTC |
| e756450 | Eddie Belter | 19 September 2012, 20:09:47 UTC | GMT LIMS APIPE: rename fix pidfa params to fir pse params; update class info and help | 19 September 2012, 20:09:47 UTC |
| 4a94cba | Eddie Belter | 19 September 2012, 20:05:34 UTC | Fix PIDFA params: mv inst data to be param for all | 19 September 2012, 20:05:43 UTC |
| 0bbb52e | Eddie Belter | 19 September 2012, 18:35:57 UTC | Microarray Extract: update snp id column setting b/c of swithc to switch to 137 | 19 September 2012, 18:38:53 UTC |
| 215c24c | dmorton | 19 September 2012, 18:36:32 UTC | Clean up MergeAndFixVcfs.t | 19 September 2012, 18:37:29 UTC |
| c4792db | Malachi Griffith | 19 September 2012, 18:22:37 UTC | Reorganize clin-seq update-analysis and add archiving checks, somatic-variation model creation, etc. | 19 September 2012, 18:22:37 UTC |
| d38a453 | Dave Larson | 19 September 2012, 17:59:16 UTC | added some pod | 19 September 2012, 17:59:26 UTC |
| 7fa4193 | Christopher C. Harris | 19 September 2012, 17:51:00 UTC | fix capitalizaton | 19 September 2012, 17:52:25 UTC |
| 829ecc0 | Nathan Dees | 19 September 2012, 17:00:28 UTC | fixed typo in PIs | 19 September 2012, 17:00:28 UTC |
| afc82c8 | Nathan Dees | 19 September 2012, 16:56:32 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 September 2012, 16:56:32 UTC |
| 4785d5b | Nathan Dees | 19 September 2012, 16:56:28 UTC | fixed typo in PIs | 19 September 2012, 16:56:28 UTC |
| 21b1eab | Jason Walker | 19 September 2012, 16:52:29 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 September 2012, 16:52:29 UTC |
| 5cbb89f | Jason Walker | 19 September 2012, 16:52:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 September 2012, 16:52:13 UTC |
| d2da2fd | Jason Walker | 19 September 2012, 16:52:09 UTC | Add a filter to limit genes/transcripts by gene biotype. Also increase the default ref-cov RAM to 16GB. | 19 September 2012, 16:52:09 UTC |
| 421378c | Christopher C. Harris | 19 September 2012, 16:51:44 UTC | commits to make the pipeline handle 2 denovo alleles in one line | 19 September 2012, 16:51:44 UTC |
| f4d4c68 | Obi Griffith | 19 September 2012, 00:34:17 UTC | Numerous fixes and updates to importers | 19 September 2012, 00:34:17 UTC |
| 94eb960 | dmorton | 18 September 2012, 22:53:11 UTC | pp view can show alignment_strategies Plus cleaned up the code a bit. | 18 September 2012, 22:55:02 UTC |
| b05f86b | Eddie Belter | 18 September 2012, 22:24:07 UTC | AQID: rm max pses param; overload inst data attr in load_lims test; update whitelist | 18 September 2012, 22:24:19 UTC |
| f69a780 | Ben Oberkfell | 18 September 2012, 22:17:41 UTC | Merge branch 'master' of git:/srv/git/genome | 18 September 2012, 22:17:41 UTC |
| 0ec854d | Ben Oberkfell | 18 September 2012, 22:15:59 UTC | disable this test because it takes too long to run | 18 September 2012, 22:15:59 UTC |
| 5361554 | Travis Abbott | 18 September 2012, 22:14:56 UTC | specify reference sequence for tigra-sv test | 18 September 2012, 22:15:34 UTC |
| af1c4c2 | Chris Miller | 18 September 2012, 22:04:34 UTC | fix to indel VAF reporting | 18 September 2012, 22:07:20 UTC |
| 57ed03a | Nathaniel Nutter | 18 September 2012, 21:37:49 UTC | update version for release | 18 September 2012, 21:37:59 UTC |
| 4cdba95 | Thomas Mooney | 18 September 2012, 21:14:56 UTC | Update `genome model instrument-data assign` help text for clarity, typos. | 18 September 2012, 21:14:56 UTC |
| c4e00f2 | Nathaniel Nutter | 18 September 2012, 20:43:03 UTC | get_with_lock only gets lock if object does not exist Only try with lock if object does not exist since locking causes a performance hit. It is assumed that if an object is found it is complete. If this is a bad assumption then we need to add a status to SoftwareResults. Please please work. | 18 September 2012, 21:10:04 UTC |
| 7924917 | Thomas Mooney | 18 September 2012, 20:20:42 UTC | Bump the memory request from 1GB to 2GB on GenePrediction::Bacterial. | 18 September 2012, 20:20:42 UTC |
| 584e2a7 | Jason Walker | 18 September 2012, 20:09:51 UTC | Updates to the DifferentialExpression pipeline to run cuffdiff and cuffcompare | 18 September 2012, 20:09:51 UTC |
| d375d2a | Jason Walker | 18 September 2012, 20:08:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 September 2012, 20:08:07 UTC |
| 41293a0 | Jason Walker | 18 September 2012, 20:07:58 UTC | A command to parse cuffdiff output and run through the Bioconductor R library, SPIA | 18 September 2012, 20:07:58 UTC |
| deb840d | Ben Oberkfell | 18 September 2012, 20:05:58 UTC | dont need to use above here | 18 September 2012, 20:05:58 UTC |
| b9f0436 | Ben Oberkfell | 18 September 2012, 19:38:20 UTC | must use a fully qualified class name here | 18 September 2012, 19:38:20 UTC |
| 451d9a6 | apregier | 18 September 2012, 19:14:50 UTC | Merge branch 'updated' into gb_master | 18 September 2012, 19:14:50 UTC |
| 81fbd02 | apregier | 18 September 2012, 19:13:55 UTC | Deduplicate annotated variant lists in somatic variation | 18 September 2012, 19:14:11 UTC |
| b1bb78e | dmorton | 18 September 2012, 18:51:22 UTC | added libconfig-inifiles-perl to genome-shapshot-deps perl | 18 September 2012, 18:51:22 UTC |
| 212d6be | John Martin | 18 September 2012, 18:35:12 UTC | adding supporting scripts for HMP processing pipeline into repository | 18 September 2012, 18:35:12 UTC |
| c1a562b | Nathan Dees | 18 September 2012, 18:08:21 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 September 2012, 18:08:21 UTC |
| 267a854 | Nathan Dees | 18 September 2012, 18:08:14 UTC | changed grant information | 18 September 2012, 18:08:14 UTC |
| 1547661 | David Morton | 17 September 2012, 22:10:38 UTC | Show notes and error-log-paths in gmb view | 18 September 2012, 17:56:13 UTC |
| 61b536d | David Morton | 17 September 2012, 20:13:18 UTC | genome model build view inherits from Viewer | 18 September 2012, 17:56:12 UTC |
| c687c61 | David Morton | 17 September 2012, 19:48:46 UTC | Make individual and pp view inherit from Viewer Add default processing-profiles for individual view (for filtering) Cosmetic improvements to individual view | 18 September 2012, 17:56:12 UTC |
| 96038a6 | David Morton | 17 September 2012, 19:47:57 UTC | Make base class for 'view' type commands. | 18 September 2012, 17:56:12 UTC |
| c02af0f | David Morton | 14 September 2012, 18:21:13 UTC | Lean on Strelka to parse strelka params in pp view | 18 September 2012, 17:56:12 UTC |
| 616e90b | David Morton | 14 September 2012, 18:19:20 UTC | Make Strelka Detector more smart about params Instead of having to specify all params, you only have to specify params that are not default. | 18 September 2012, 17:56:12 UTC |
| 5979329 | Nathan Dees | 18 September 2012, 16:43:14 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 September 2012, 16:43:14 UTC |
| 0733bd0 | Nathan Dees | 18 September 2012, 16:43:11 UTC | changed grant information | 18 September 2012, 16:43:11 UTC |
| 112993b | Brian Derickson | 18 September 2012, 14:45:24 UTC | added is_archived method to buildl | 18 September 2012, 14:45:24 UTC |
| aad0f96 | Malachi Griffith | 18 September 2012, 04:38:50 UTC | Add subroutines to clin-seq analysis-update for somatic-variation models | 18 September 2012, 04:38:50 UTC |
| 45bba0c | Brian Derickson | 18 September 2012, 01:56:47 UTC | fixed method name | 18 September 2012, 01:56:47 UTC |
| 848cee1 | Brian Derickson | 17 September 2012, 22:24:05 UTC | added archivable method to builds, which just checks the archivable status of the data directoryallocation | 17 September 2012, 22:24:10 UTC |
| 0af8596 | Brian Derickson | 17 September 2012, 22:23:40 UTC | attempting to unarchive an allocation that is not archived is no longer a fatal error | 17 September 2012, 22:24:09 UTC |
| bf4e3af | Justin Lolofie | 17 September 2012, 21:46:54 UTC | total disk usage and archive info | 17 September 2012, 21:46:54 UTC |
| b6c09d0 | Travis Abbott | 17 September 2012, 21:09:15 UTC | correctly output genes with null p-values in burden test | 17 September 2012, 21:09:15 UTC |
| 5492c2c | Travis Abbott | 17 September 2012, 21:03:21 UTC | convert VEP annotation priority from hash to array | 17 September 2012, 21:04:06 UTC |
| 7b51721 | Thomas Mooney | 17 September 2012, 21:00:55 UTC | Strip the trailing L off of certain cell types. | 17 September 2012, 21:03:50 UTC |
| e319a6d | Dave Larson | 17 September 2012, 21:01:00 UTC | added back in unfiltered qqplots | 17 September 2012, 21:01:08 UTC |
| f20b2f7 | Dave Larson | 17 September 2012, 18:12:57 UTC | made vcf-report output files available via build | 17 September 2012, 21:01:07 UTC |
| 6207893 | Dave Larson | 17 September 2012, 16:30:19 UTC | add in the removal of rare variants from the qqplots | 17 September 2012, 21:01:07 UTC |
| be8f0ef | Malachi Griffith | 17 September 2012, 20:54:21 UTC | Bring clin-seq ad hoc druggable genes heatmap code under version control | 17 September 2012, 20:54:21 UTC |
| 7796fca | Malachi Griffith | 17 September 2012, 20:53:38 UTC | Continued development of clin-seq update-analysis | 17 September 2012, 20:53:38 UTC |
| b9cbce6 | Travis Abbott | 17 September 2012, 20:50:38 UTC | add VEP support to gmt graph mutation-diagram | 17 September 2012, 20:51:10 UTC |
| c355e87 | Thomas Mooney | 17 September 2012, 20:08:53 UTC | Avoid spurious indication the calculated property wasn't specified. Update the LIMS whitelist to reflect two new lines. | 17 September 2012, 20:08:53 UTC |
| fcc285d | Thomas Mooney | 17 September 2012, 19:15:59 UTC | Declare the calculated property as calculated so it doesn't get default magic. | 17 September 2012, 19:15:59 UTC |
| a9815aa | Dan Koboldt | 17 September 2012, 19:12:38 UTC | Updates to perform FET on rare deleterious table | 17 September 2012, 19:12:38 UTC |
| 357366c | Dan Koboldt | 17 September 2012, 19:12:20 UTC | Directory for Beagle tools | 17 September 2012, 19:12:20 UTC |
