| 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 |
| 31675b3 | Travis Abbott | 13 September 2012, 18:13:23 UTC | add sample_names accessor to clinical data object | 13 September 2012, 21:39:08 UTC |
| e54db12 | Eddie Belter | 13 September 2012, 16:41:27 UTC | AQID de novo, gm, mc16s tests: rm refs to pses! | 13 September 2012, 21:39:08 UTC |
| b60fad6 | Eddie Belter | 13 September 2012, 16:31:23 UTC | AQID: QIDFGM no longer required to process inst data | 13 September 2012, 21:39:08 UTC |
| f678817 | Eddie Belter | 12 September 2012, 21:39:02 UTC | AQID: Rm all PSE refs except those needed for the transition period | 13 September 2012, 21:39:08 UTC |
| 2067478 | Eddie Belter | 12 September 2012, 20:38:47 UTC | AQID: made execute completely inst data centric | 13 September 2012, 21:39:08 UTC |
| cc561e6 | Eddie Belter | 12 September 2012, 20:12:22 UTC | AQID: load_pses is now _load_instrument_data; made execute more isnt data centric | 13 September 2012, 21:39:08 UTC |
| 57c6446 | Eddie Belter | 12 September 2012, 19:56:55 UTC | AQID: make load_pses more inst data centric | 13 September 2012, 21:39:08 UTC |
| 5400661 | Eddie Belter | 12 September 2012, 19:15:59 UTC | AQID: rm max_pses_to_check param | 13 September 2012, 21:39:07 UTC |
| 3b02e78 | Eddie Belter | 12 September 2012, 17:21:06 UTC | AQID: rm pse_id use from one test | 13 September 2012, 21:39:07 UTC |
| b2a4e49 | Eddie Belter | 12 September 2012, 16:49:44 UTC | AQID: rm pse_id option | 13 September 2012, 21:39:07 UTC |
| a86a852 | Eddie Belter | 12 September 2012, 16:38:51 UTC | AQID: consolidate default pp for de novo | 13 September 2012, 21:39:07 UTC |
| 0513aad | Eddie Belter | 12 September 2012, 16:35:57 UTC | AQID: consolidate default pp for ref align | 13 September 2012, 21:39:07 UTC |
| 7e2d385 | Eddie Belter | 11 September 2012, 22:52:23 UTC | AQID: Made separate method for setting tgi lims status to failed | 13 September 2012, 21:39:07 UTC |
| 4586282 | Eddie Belter | 11 September 2012, 22:12:04 UTC | AQID: getting pp and ref seqs in one place | 13 September 2012, 21:39:07 UTC |
| 26e7992 | Eddie Belter | 11 September 2012, 20:10:43 UTC | AQID: switch from ref seq names to ids | 13 September 2012, 21:39:07 UTC |
| 4e3c04d | Eddie Belter | 11 September 2012, 19:38:39 UTC | AQID: mv additional 454 logic into add pp to pse from execute | 13 September 2012, 21:39:06 UTC |
| f8308b9 | Eddie Belter | 11 September 2012, 19:24:46 UTC | AQID: Move checking pps added to pse out of add pp to pse | 13 September 2012, 21:39:06 UTC |
| c8160fa | Brian Derickson | 13 September 2012, 17:42:51 UTC | added INT/TERM handlers during archive/unarchive that kills HPSS job and cleans up archive directory | 13 September 2012, 21:39:06 UTC |
| 5767316 | Brian Derickson | 13 September 2012, 16:45:53 UTC | new method that kills a given LSF job | 13 September 2012, 21:39:06 UTC |
| eaf56f8 | Travis Abbott | 13 September 2012, 17:21:09 UTC | fix generation of Sample_List.txt sample names from the vcf file were being compared to sample objects from the population group rather than their names. | 13 September 2012, 21:39:06 UTC |
| 8fa26ff | Travis Abbott | 13 September 2012, 17:05:53 UTC | eliminate uninitialized string warning | 13 September 2012, 21:39:06 UTC |
| ac932c4 | Nathan Dees | 13 September 2012, 16:21:18 UTC | added doc to describe funding and manuscript citation | 13 September 2012, 21:39:06 UTC |
| ffcf365 | Nathan Dees | 13 September 2012, 16:20:23 UTC | Fixed case if one puts NA in the model file in the variant / gene name column | 13 September 2012, 21:39:06 UTC |
| ab2465e | David Morton | 13 September 2012, 01:48:10 UTC | Cosmetic improvement to genome pp view clean up whitespace around strelka args. | 13 September 2012, 21:39:06 UTC |
| f6bb57b | David Morton | 13 September 2012, 01:47:05 UTC | Cleanup tree_to_string fn | 13 September 2012, 21:39:05 UTC |
| 9503228 | David Morton | 12 September 2012, 22:23:52 UTC | Created genome individual view The most likely user will be people looking at individuals to see if they are candidates for clin-seq, so defaults are made sensible for that purpose. | 13 September 2012, 21:39:05 UTC |
| 368160d | David Morton | 12 September 2012, 22:23:15 UTC | genome pp view has option for showing model info | 13 September 2012, 21:39:05 UTC |
| 19fc038 | David Morton | 12 September 2012, 20:43:26 UTC | genome pp view uses IO::Handle refactor that is cleaner and makes view more responsive because it prints lines immediately instead of big chunks at a time. | 13 September 2012, 21:39:05 UTC |
| a851984 | David Morton | 12 September 2012, 20:42:02 UTC | Make Utility::Text export fns And various small fn fixes. | 13 September 2012, 21:39:05 UTC |
| 1e48c23 | Mark Burnett | 13 September 2012, 15:10:48 UTC | Improve UCSC table resolution for builds | 13 September 2012, 21:39:05 UTC |
| b00266b | Travis Abbott | 13 September 2012, 03:44:35 UTC | always validate clinical data in phenotype correlation. | 13 September 2012, 21:39:05 UTC |
| 95fcfa7 | Travis Abbott | 13 September 2012, 02:24:20 UTC | add vcf identifiers to variant names in varmatrix | 13 September 2012, 21:39:05 UTC |
| 1edce2a | Travis Abbott | 13 September 2012, 01:56:37 UTC | ClinicalData: coerce_to_binary => convert_attr_to_factor In PhenotypeCorrelation's ClinicalData class, the coerce_to_binary function has been updated to support converting into factors with an arbitrary number of specified levels. Example: $cd->coerce_to_binary($name, zero => "x", one => "y") is now $cd->convert_attr_to_factor($name, levels => ["x", "y"]) Both of these verify that attr $name contains only 'x', 'y', and undef, and converts x => 0, y => 1. | 13 September 2012, 21:39:04 UTC |
| 470d6e8 | Obi Griffith | 13 September 2012, 00:47:33 UTC | Fixed case of HopkinsGroom category | 13 September 2012, 21:39:04 UTC |
| ffe5b70 | Obi Griffith | 12 September 2012, 23:44:07 UTC | wrote new importer for Hopkins and Groom dataset | 13 September 2012, 21:39:04 UTC |
| d9a84dd | Malachi Griffith | 12 September 2012, 23:01:25 UTC | Added various subroutines for examining status of reference alignment models | 13 September 2012, 21:39:04 UTC |
| 77ac44b | Mark Burnett | 12 September 2012, 21:37:42 UTC | Fix bugs with ImportedAnnotation gap file fetching | 13 September 2012, 21:39:04 UTC |
| 77d9d07 | Mark Burnett | 12 September 2012, 21:36:05 UTC | Add ability to get gap data from multiple tables | 13 September 2012, 21:39:04 UTC |
