| 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 |
| 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 |
| 3859094 | Nathan Dees | 17 September 2012, 18:39:08 UTC | changed it to music in the license section | 17 September 2012, 18:39:08 UTC |
| e68ff77 | Thomas Mooney | 17 September 2012, 17:55:31 UTC | Speed up view by pre-loading data in fewer queries. | 17 September 2012, 17:55:31 UTC |
| 6cd527a | Eddie Belter | 17 September 2012, 16:43:36 UTC | MC16s: update entire run email | 17 September 2012, 16:43:36 UTC |
| 89f1ed1 | Eddie Belter | 17 September 2012, 16:35:18 UTC | MC16s Run Status: update pp doc | 17 September 2012, 16:35:18 UTC |
| 7ea23c3 | Dan Koboldt | 17 September 2012, 15:44:28 UTC | Updates to human genetics analysis tools | 17 September 2012, 15:44:28 UTC |
| 25ab32e | Dan Koboldt | 17 September 2012, 15:42:45 UTC | New tools for human genetics analysis | 17 September 2012, 15:42:45 UTC |
| 6363cf2 | apregier | 17 September 2012, 15:33:40 UTC | Merge branch 'updated' into gb_master | 17 September 2012, 15:33:40 UTC |
| ad9fdab | apregier | 17 September 2012, 15:32:08 UTC | CHANGELOG Default human dbsnp build is 137 | 17 September 2012, 15:33:25 UTC |
| 748b4af | APipe Tester | 17 September 2012, 15:15:12 UTC | updated ur submodule to 8376d66 | 17 September 2012, 15:15:12 UTC |
| 81e9d0f | Justin Lolofie | 17 September 2012, 14:58:43 UTC | better error msg better ret value | 17 September 2012, 14:58:43 UTC |
| 2483b85 | APipe Tester | 17 September 2012, 13:55:21 UTC | updated ur submodule to c3d459b | 17 September 2012, 13:55:21 UTC |
| 43d0567 | Obi Griffith | 16 September 2012, 23:05:10 UTC | Improved usage example for Entrez Importer | 16 September 2012, 23:05:10 UTC |
| 97ed2d2 | Obi Griffith | 16 September 2012, 23:02:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 September 2012, 23:02:30 UTC |
| 376da72 | Dave Larson | 14 September 2012, 22:27:27 UTC | remove some unnecessary includes and include attribution | 14 September 2012, 22:27:27 UTC |
| 0c280d3 | Dave Larson | 14 September 2012, 22:25:16 UTC | simple module to filter clinical correlation results by MAF | 14 September 2012, 22:25:24 UTC |
| a0e48c3 | Ian Ferguson | 14 September 2012, 22:09:50 UTC | Updated location of C utility for ErrorRate.pm | 14 September 2012, 22:10:11 UTC |
| 2cd7cde | Justin Lolofie | 14 September 2012, 21:43:22 UTC | unarchive allocations for a build | 14 September 2012, 21:43:22 UTC |
| e8e7219 | Eddie Belter | 14 September 2012, 21:21:52 UTC | AQID: update test count for validation | 14 September 2012, 21:38:35 UTC |
| 4810163 | Eddie Belter | 14 September 2012, 21:17:52 UTC | AQID: make validation test PSE free | 14 September 2012, 21:38:35 UTC |
| bba93e0 | Eddie Belter | 14 September 2012, 21:17:28 UTC | AQID: override GSC::PSE::get in mc16s test | 14 September 2012, 21:38:35 UTC |
| 975dd9f | Eddie Belter | 14 September 2012, 21:04:02 UTC | AQID: add call to GSC::PSE class to avoid editing the whitelist during refactoring | 14 September 2012, 21:38:34 UTC |
| 6ff5242 | Eddie Belter | 14 September 2012, 19:07:55 UTC | AQID: stop preloading or wahtever | 14 September 2012, 21:38:34 UTC |
| b0150a1 | Obi Griffith | 14 September 2012, 20:41:02 UTC | Updated all importers to use consistent default location for intermediate TSV files | 14 September 2012, 20:41:02 UTC |
| d892f2a | Kyung Kim | 14 September 2012, 20:20:48 UTC | Update to filter out reads that become 10 or less bases after clipping since such reads will fail further processing down the stream | 14 September 2012, 20:20:48 UTC |
| e21fde3 | Obi Griffith | 14 September 2012, 20:16:13 UTC | Created new generic category for Druggable Genome lists | 14 September 2012, 20:16:13 UTC |
| 3ae2e57 | Jim Weible | 14 September 2012, 19:08:51 UTC | tool to removed paired reads from a namesorted bam | 14 September 2012, 19:08:59 UTC |
| 13fa38c | Jim Weible | 14 September 2012, 19:07:49 UTC | clarify help text | 14 September 2012, 19:08:59 UTC |
| 44334aa | Eddie Belter | 14 September 2012, 18:57:29 UTC | AQID: rm PSEParam from white list | 14 September 2012, 18:57:37 UTC |
| 84436c4 | Eddie Belter | 14 September 2012, 18:57:14 UTC | AQID: rm instrument_data_type | 14 September 2012, 18:57:36 UTC |
| a60e6d6 | Eddie Belter | 14 September 2012, 18:52:19 UTC | AQID: update whitelist | 14 September 2012, 18:57:36 UTC |
| bd392da | Eddie Belter | 14 September 2012, 18:48:47 UTC | AQID: rm root ref seq method | 14 September 2012, 18:57:36 UTC |
| 8c49968 | Nathan Dees | 14 September 2012, 18:55:15 UTC | updated the call to bam-readcount with --variant-file | 14 September 2012, 18:55:15 UTC |
| 8f9a89d | Eddie Belter | 14 September 2012, 18:42:55 UTC | AQID: fix indent | 14 September 2012, 18:43:02 UTC |
| d3ea947 | Brian Derickson | 14 September 2012, 18:41:35 UTC | added a few new abbreviations | 14 September 2012, 18:41:35 UTC |
| 0926894 | Ian Ferguson | 14 September 2012, 18:22:00 UTC | Updated archive_path for raw sra download format in ID/Imported.pm Updated _archive_file_name and archive_path handling of 'raw sra download' formatted instrument data. It now attempts to output the path to a directory if we happen to find a directory structure instead of a single .sra file. | 14 September 2012, 18:25:21 UTC |
| b6f2efb | Travis Abbott | 14 September 2012, 17:33:18 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 September 2012, 17:33:18 UTC |
| a2e10da | Travis Abbott | 14 September 2012, 17:31:56 UTC | submodules -> latest | 14 September 2012, 17:32:59 UTC |
| 95d0815 | Jason Walker | 14 September 2012, 16:55:52 UTC | remove the merge lines after switching to new git repo | 14 September 2012, 16:55:52 UTC |
| 8308db0 | Ian Ferguson | 14 September 2012, 15:39:57 UTC | Updated ID/Imported->archive_path for raw sra Updated archive_path() in InstrumentData::Imported to handle instrument data with the 'raw sra download' format. This only handles instrument data that has a directory structure like "SRR######/SRR######.sra". Some (older?) instrument data in the 'raw sra download' format instead have a complex directory structure with multiple files. archive_path() will continue to die in those situations. | 14 September 2012, 15:39:57 UTC |
| 535d5bc | Jim Weible | 14 September 2012, 15:07:36 UTC | cleanup | 14 September 2012, 15:07:51 UTC |
| 0ee2ed9 | Jason Walker | 14 September 2012, 15:00:40 UTC | Copy changes from old git repo. Mostly related to a new model type for differential expression of RNA-Seq data. | 14 September 2012, 15:00:40 UTC |
| 7bda7e4 | Scott Smith | 14 September 2012, 00:24:52 UTC | cosmetic update to README | 14 September 2012, 00:24:52 UTC |
| 78e832c | David Morton | 13 September 2012, 23:30:40 UTC | Clean up params in genome pp view | 13 September 2012, 23:30:40 UTC |
| 0e479e1 | Obi Griffith | 13 September 2012, 23:02:04 UTC | final changes before rebase, removed missing categories from HopkinsGroom import | 13 September 2012, 23:05:32 UTC |
| d6d4e80 | Thomas Mooney | 13 September 2012, 20:57:04 UTC | Use __meta__ instead of UR::Object::Type->get(); This returns more quickly when the class has already been loaded and otherwise loads the Type object as needed. | 13 September 2012, 21:39:09 UTC |
| 83d09b9 | Obi Griffith | 13 September 2012, 20:29:01 UTC | added code to eliminate backslashes from human readable category names | 13 September 2012, 21:39:09 UTC |
| c3b82bf | Kyung Kim | 13 September 2012, 20:26:41 UTC | Bug fix so empty fasta file is not created for blast when blast output from prev staged, pooled and split. This was possible when number of reads in pooled file is a multiple of number of reads to split | 13 September 2012, 21:39:09 UTC |
| 2278a74 | Nathan Dees | 13 September 2012, 19:50:04 UTC | added doc sub for authors | 13 September 2012, 21:39:09 UTC |
| 65bac01 | Eddie Belter | 13 September 2012, 19:28:23 UTC | AQID: use is_rna on sample instead of internal method | 13 September 2012, 21:39:09 UTC |
| 92b064b | Eddie Belter | 13 September 2012, 19:25:39 UTC | Sample: add is_rna to class def; update tests | 13 September 2012, 21:39:09 UTC |
| 7571255 | Kyung Kim | 13 September 2012, 19:21:20 UTC | Update to work for velvet versions deployed in usr/bin | 13 September 2012, 21:39:09 UTC |
| 1e46278 | Travis Abbott | 13 September 2012, 19:16:28 UTC | verify that clinical data, vcf, and pop group have same samples phenotype correlation now checks that the intersection of samples in the clinical data, multisample vcf, and population group is non-empty before doing anything serious. | 13 September 2012, 21:39:08 UTC |
