| de0db0d | Thomas Mooney | 11 August 2014, 17:41:32 UTC | Initial version of a FeatureList merge tool. BED-merging code taken from GSCApp::BEDFile. | 11 August 2014, 22:54:41 UTC |
| a148dbf | apregier | 11 August 2014, 22:34:31 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 22:34:31 UTC |
| 25c11cb | apregier | 11 August 2014, 22:33:49 UTC | If there is no information about the af for an allele, always pass the filter | 11 August 2014, 22:33:49 UTC |
| 3bca94b | apregier | 11 August 2014, 22:27:11 UTC | When no CAF is available, it should pass | 11 August 2014, 22:27:11 UTC |
| ae980b3 | apregier | 11 August 2014, 22:16:57 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 22:16:57 UTC |
| fb3b1fe | apregier | 11 August 2014, 22:14:15 UTC | Revert "Revert "Bump vcf_version due to a bump in the default joinx version"" This reverts commit 578c984a0092b71b2bf8c143897cdcdcedc14421. No takesies backsies!!! | 11 August 2014, 22:14:15 UTC |
| c77d7a0 | Thomas Mooney | 11 August 2014, 22:11:49 UTC | Make generic SR expunge process for when deleting an object. Use it for InstrumentData and Sample deletion. | 11 August 2014, 22:11:49 UTC |
| 9675e04 | apregier | 11 August 2014, 21:54:43 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 21:54:43 UTC |
| 99f6fc4 | apregier | 11 August 2014, 21:50:46 UTC | Make verify bam id code respect test name and add user relationship | 11 August 2014, 21:51:38 UTC |
| 62394d6 | Eddie Belter | 11 August 2014, 19:48:48 UTC | File VCF: rm dumper statement | 11 August 2014, 19:49:09 UTC |
| 9f0c7d3 | apregier | 11 August 2014, 19:35:53 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 19:35:53 UTC |
| 7447f1d | apregier | 11 August 2014, 19:31:06 UTC | snv detection strategy is optional | 11 August 2014, 19:33:25 UTC |
| 578c984 | dmorton | 11 August 2014, 19:20:48 UTC | Revert "Bump vcf_version due to a bump in the default joinx version" This reverts commit 5993ebd598c94bba2847bcd8cdcc17a049ca7311. | 11 August 2014, 19:20:48 UTC |
| 5993ebd | dmorton | 11 August 2014, 19:06:22 UTC | Bump vcf_version due to a bump in the default joinx version | 11 August 2014, 19:06:22 UTC |
| 6ac75e1 | Thomas Mooney | 11 August 2014, 15:22:34 UTC | Use build factory for benefit of setup_reference_sequence_build. | 11 August 2014, 15:22:34 UTC |
| 247869f | APipe Tester | 09 August 2014, 12:17:13 UTC | Updated `gmt` tab completion. | 09 August 2014, 12:17:13 UTC |
| 0ef1383 | APipe Tester | 09 August 2014, 12:16:31 UTC | Updated `genome` tab completion. | 09 August 2014, 12:16:31 UTC |
| 8a00921 | Charles Lu | 08 August 2014, 21:33:26 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 08 August 2014, 21:33:26 UTC |
| 9b12b69 | Charles Lu | 08 August 2014, 21:33:18 UTC | fixed few bugs with the plot coverage tool. Added --highlight option to the tool | 08 August 2014, 21:33:18 UTC |
| 6227599 | Adam Coffman | 08 August 2014, 20:26:11 UTC | return empty string on method mismatch instead of shift // empty | 08 August 2014, 20:26:11 UTC |
| 55e4f0d | Adam Coffman | 08 August 2014, 20:24:12 UTC | check if a method exists before calling it: AUE-291 | 08 August 2014, 20:24:12 UTC |
| 139fe24 | Gabriel Sanderson | 25 July 2014, 19:58:39 UTC | No longer die when we find no gene. Instead we print a summary of transcript types that contained no gene at the end. | 08 August 2014, 19:54:10 UTC |
| b91ef7d | Gabriel Sanderson | 25 July 2014, 19:51:01 UTC | make transient properties optional | 08 August 2014, 19:54:09 UTC |
| cedd706 | Gabriel Sanderson | 23 June 2014, 22:52:30 UTC | Add a plan and resource file for rnaseq variant filtering and reporting It is not yet possible to do translated inputs for experts, so we must put the tumor sample name in the resource file (twice) for the fpkm expert. | 08 August 2014, 19:54:08 UTC |
| 3d21aa9 | Gabriel Sanderson | 23 June 2014, 22:50:40 UTC | If object_errors are encountered, detail the module. There may be a better way of doing this, but this is an improvement for now. Previous to this fix, when UR returned missing/invalid property errors, we would have no clue which module in the plan contained the problem. | 08 August 2014, 19:54:08 UTC |
| d4c3e2e | Adam Coffman | 08 August 2014, 19:48:41 UTC | add accessors for model->config_item | 08 August 2014, 19:48:41 UTC |
| 80aa587 | Adam Coffman | 08 August 2014, 19:21:55 UTC | schema change for tracking config item -> model links in AnP | 08 August 2014, 19:21:55 UTC |
| aaeb65a | apregier | 08 August 2014, 18:14:42 UTC | Merge branch 'copy' into gb_master | 08 August 2014, 18:14:42 UTC |
| 8052e4c | apregier | 08 August 2014, 18:13:16 UTC | Gatk logic has moved around a bit. | 08 August 2014, 18:13:16 UTC |
| 9dc037b | Gabriel Sanderson | 08 August 2014, 16:38:00 UTC | remove redundant get_readcount_entry call | 08 August 2014, 17:31:07 UTC |
| 8a79cf9 | Gabriel Sanderson | 07 August 2014, 22:56:23 UTC | Interpreters return null interpretations when appropriate | 08 August 2014, 17:31:06 UTC |
| 5f87b4c | Gabriel Sanderson | 07 August 2014, 22:38:43 UTC | remove redundant method call | 08 August 2014, 17:31:05 UTC |
| 261ae80 | Gabriel Sanderson | 07 August 2014, 21:43:59 UTC | Refactor logic for returning a null interpretation to the base class. | 08 August 2014, 17:31:05 UTC |
| 8925905 | Gabriel Sanderson | 07 August 2014, 20:20:10 UTC | Auto pass all alts for a sample when we have no information. made pass_all_sample_alts method. Use it. | 08 August 2014, 17:31:04 UTC |
| f52bfec | APipe Tester | 08 August 2014, 12:16:44 UTC | Updated `genome` tab completion. | 08 August 2014, 12:16:44 UTC |
| 93149f9 | APipe Tester | 08 August 2014, 12:15:07 UTC | Updated class browser cache. | 08 August 2014, 12:15:07 UTC |
| ff58a0c | Chris Miller | 08 August 2014, 05:39:30 UTC | tumor and normal labels were swapped | 08 August 2014, 05:39:30 UTC |
| 51dd70b | Thomas Mooney | 07 August 2014, 22:56:36 UTC | Fix test: build requires more information to be defined now. | 07 August 2014, 22:56:36 UTC |
| a30744e | Thomas Mooney | 07 August 2014, 18:32:06 UTC | New PP parameters to allow explicitly skipping validation steps. | 07 August 2014, 22:44:03 UTC |
| e739441 | Eddie Belter | 07 August 2014, 21:25:25 UTC | File VCF: update dbsnp parser to handle R info type number | 07 August 2014, 21:51:31 UTC |
| 80e604a | Eddie Belter | 07 August 2014, 20:52:30 UTC | GM: reader for instdata w/ annotation uses entry add_allele method | 07 August 2014, 21:51:30 UTC |
| b3e401f | Eddie Belter | 07 August 2014, 20:22:16 UTC | File VCF: add_allele adds info to A & R fields | 07 August 2014, 21:51:30 UTC |
| 15c7ab1 | Eddie Belter | 07 August 2014, 20:02:07 UTC | File VCF: updated info_for_allele to return info for ref info type R | 07 August 2014, 21:51:29 UTC |
| 81091aa | Eddie Belter | 07 August 2014, 19:15:29 UTC | File VCF: update to vcf4.2 using Number=R representing on value per ref and alts | 07 August 2014, 21:51:29 UTC |
| d1e843b | Eddie Belter | 07 August 2014, 18:55:12 UTC | File VCF: add_allele method to add allele to entry | 07 August 2014, 21:51:27 UTC |
| a95fff2 | Susanna Siebert | 07 August 2014, 19:30:29 UTC | Fixed bug in min_coverage_observed calculation | 07 August 2014, 19:31:03 UTC |
| 606b60f | Thomas Mooney | 06 August 2014, 22:59:29 UTC | Skip pending AnPs early like we do held ones. This prevents the pending instrument data from shutting out other work CQID could be doing. | 06 August 2014, 22:59:29 UTC |
| 41ad296 | Gabriel Sanderson | 05 August 2014, 22:08:55 UTC | updated mentions of joinx1.8 to 1.9 in test cases | 05 August 2014, 22:08:55 UTC |
| 6835e7a | Gabriel Sanderson | 05 August 2014, 20:46:58 UTC | update plans to use joinx 1.9 | 05 August 2014, 20:46:58 UTC |
| 06cf7ea | Gabriel Sanderson | 05 August 2014, 20:27:13 UTC | update default joinx version to 1.9 | 05 August 2014, 20:27:33 UTC |
| 5cc0b5c | Susanna Siebert | 05 August 2014, 19:32:49 UTC | Eval the call to Genome::Sys->rename Genome::Sys->rename will die if it fails which will prevent the callback from working and retrying. | 05 August 2014, 19:43:43 UTC |
| f057f05 | apregier | 05 August 2014, 19:36:40 UTC | Merge branch 'copy' into gb_master | 05 August 2014, 19:36:40 UTC |
| 0e88a4d | apregier | 05 August 2014, 19:05:15 UTC | Skip entries with messed up CAF entries - they will simply not be counted toward the af_count metric | 05 August 2014, 19:34:34 UTC |
| 032ba1c | Adam Coffman | 05 August 2014, 17:50:04 UTC | make lack of lq variants in tiering non-fatal | 05 August 2014, 17:50:04 UTC |
| a162e4c | Thomas Mooney | 05 August 2014, 15:50:00 UTC | Use a raw SQL query to efficiently populate this view. The old version was taking > 3000sec and 3 GB of memory, so this will get us by in the meanwhile. | 05 August 2014, 15:50:00 UTC |
| 2651720 | Thomas Mooney | 05 August 2014, 13:32:25 UTC | New classes to define tags and to link them to profile items. | 05 August 2014, 13:32:25 UTC |
| e7dab07 | Thomas Mooney | 05 August 2014, 13:01:25 UTC | More efficient query for the count in the model-group display name. | 05 August 2014, 13:01:25 UTC |
| 6fa6045 | Thomas Mooney | 04 August 2014, 22:25:17 UTC | Tables to support tagging of configurations in AnP Config | 04 August 2014, 22:25:17 UTC |
| f006645 | Gabriel Sanderson | 01 August 2014, 22:08:48 UTC | Handle alt_bases_for_sample and genotype_for_sample returning undef. | 01 August 2014, 22:16:06 UTC |
| 82fba5d | Gabriel Sanderson | 01 August 2014, 22:15:28 UTC | alt_bases_for_sample returns undef if no genotype found. | 01 August 2014, 22:16:05 UTC |
| 9375120 | Gabriel Sanderson | 01 August 2014, 21:15:46 UTC | Correct bug in File::Vcf::Entry. Change behavior when no sample present. File::Vcf::Entry contained a bug where the bounds of the sample index was too permissive by 1. We also now return undef instead of confessing when we have no GT information for a sample - the sample might just be '.'. Corrected an oversight in the unit test - there were not enough samples in the header for the "get genotype for sample" subtest data. And we had to correct the behavior assumptions when dying for the above. | 01 August 2014, 21:19:43 UTC |
| 1f15b9b | Feiyu Du | 01 August 2014, 21:07:17 UTC | renamed | 01 August 2014, 21:07:17 UTC |
| 49cc615 | dmorton | 01 August 2014, 20:32:36 UTC | Clean up HeaderDiff->print output for sample name diffs | 01 August 2014, 20:33:20 UTC |
| 60c9979 | Feiyu Du | 01 August 2014, 20:17:32 UTC | add vep MaxSegdupFilter | 01 August 2014, 20:17:32 UTC |
| 1a4ffb9 | apregier | 01 August 2014, 17:24:01 UTC | Merge branch 'updated' into gb_master | 01 August 2014, 17:24:01 UTC |
| 71c8fea | apregier | 01 August 2014, 16:10:06 UTC | Run reports with d30 model as base | 01 August 2014, 17:20:34 UTC |
| ebf3fa8 | apregier | 01 August 2014, 15:32:06 UTC | Use network file location for intermediate output file | 01 August 2014, 15:32:47 UTC |
| 82fdc6e | APipe Tester | 01 August 2014, 12:18:09 UTC | Updated `gmt` tab completion. | 01 August 2014, 12:18:09 UTC |
| 6713a21 | APipe Tester | 01 August 2014, 12:17:28 UTC | Updated `genome` tab completion. | 01 August 2014, 12:17:28 UTC |
| 81e9255 | APipe Tester | 01 August 2014, 12:15:39 UTC | Updated class browser cache. | 01 August 2014, 12:15:39 UTC |
| e55e803 | APipe Tester | 31 July 2014, 21:47:56 UTC | updated ur submodule to f5acb4c | 31 July 2014, 21:47:56 UTC |
| cc72c98 | apregier | 31 July 2014, 21:33:57 UTC | Merge branch 'fireteam' into gb_master | 31 July 2014, 21:33:57 UTC |
| 90fa80e | apregier | 31 July 2014, 21:31:11 UTC | Change annotate-with-readcount to take sample name This way, the tool can add an additional sample name if it doesn't already exist in the vcf file. | 31 July 2014, 21:31:11 UTC |
| 4fe08f8 | apregier | 31 July 2014, 18:47:14 UTC | Don't separately add sample name to input vcfs | 31 July 2014, 21:23:46 UTC |
| 875ac9c | Ian Ferguson | 31 July 2014, 20:44:13 UTC | Fix Cufflinks memory request during testing | 31 July 2014, 20:44:40 UTC |
| e6177d8 | Eddie Belter | 31 July 2014, 19:26:33 UTC | GMT: add gatk command tree class | 31 July 2014, 19:26:33 UTC |
| d369197 | Eddie Belter | 31 July 2014, 19:14:34 UTC | DV2: use full GATK class name to check legacy version | 31 July 2014, 19:14:34 UTC |
| 3eefca4 | apregier | 31 July 2014, 18:55:24 UTC | Merge branch 'updated' into gb_master | 31 July 2014, 18:55:24 UTC |
| f7c54fe | apregier | 30 July 2014, 17:47:56 UTC | Fix pindel sorting | 31 July 2014, 18:54:17 UTC |
| 44fd477 | Eddie Belter | 30 July 2014, 23:51:31 UTC | InstData Gatk: add -n to rusage in refine reads gatk base | 31 July 2014, 17:42:39 UTC |
| 20e31d0 | Eddie Belter | 30 July 2014, 23:47:32 UTC | InstData Gatk: update threading in indel realigner | 31 July 2014, 17:42:39 UTC |
| f69b696 | Eddie Belter | 30 July 2014, 23:44:18 UTC | InstData Gatk: specify rusage for best practices commands | 31 July 2014, 17:42:38 UTC |
| fe35a5c | Eddie Belter | 30 July 2014, 23:33:35 UTC | InstData GATK: max memory returns GB | 31 July 2014, 17:42:38 UTC |
| 706a6e6 | Eddie Belter | 15 July 2014, 17:50:44 UTC | InstData GATK: do not compare grp output from base recalibrator test | 31 July 2014, 17:42:37 UTC |
| 3e5f53d | Eddie Belter | 15 July 2014, 17:08:41 UTC | InstData GATK: set max_memory for gatk tools using Genome::Sys | 31 July 2014, 17:42:37 UTC |
| 46f1431 | Eddie Belter | 14 July 2014, 22:37:18 UTC | InstData GATK: use threading | 31 July 2014, 17:42:36 UTC |
| bbbc619 | Eddie Belter | 14 July 2014, 19:36:43 UTC | GMT GATK: use threading mix in classes as appropriate | 31 July 2014, 17:42:36 UTC |
| 8bf40bc | Eddie Belter | 14 July 2014, 19:35:27 UTC | GMT GATK: add mix in classes for threading options | 31 July 2014, 17:42:35 UTC |
| 7bb0c15 | Eddie Belter | 10 July 2014, 20:06:24 UTC | Gatk: rename the base class | 31 July 2014, 17:42:35 UTC |
| c792695 | Thomas Mooney | 31 July 2014, 13:13:17 UTC | Consistently use the build's assigned instrument data. The model's assignments may have changed (or be nonexistent!) | 31 July 2014, 13:13:46 UTC |
| 8e42bb8 | APipe Tester | 31 July 2014, 12:17:11 UTC | Updated `gmt` tab completion. | 31 July 2014, 12:17:11 UTC |
| 5dd4d4e | APipe Tester | 31 July 2014, 12:16:31 UTC | Updated `genome` tab completion. | 31 July 2014, 12:16:31 UTC |
| 942c5d0 | APipe Tester | 31 July 2014, 12:15:10 UTC | Updated class browser cache. | 31 July 2014, 12:15:10 UTC |
| 8662a4a | kmeltzst | 30 July 2014, 21:06:16 UTC | memoize bam index | 30 July 2014, 21:06:47 UTC |
| 36c8e6c | Feiyu Du | 30 July 2014, 20:55:18 UTC | update ref-align test build | 30 July 2014, 20:55:18 UTC |
| 29dc76f | kmeltzst | 30 July 2014, 20:50:13 UTC | don't make bam.index hardcoded | 30 July 2014, 20:50:13 UTC |
| 1c166df | Susanna Siebert | 30 July 2014, 18:07:14 UTC | ensure that skipping of loh is handled conistently between steps | 30 July 2014, 18:34:42 UTC |
| 68cb1c6 | Feiyu Du | 30 July 2014, 18:33:45 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 30 July 2014, 18:33:45 UTC |
| f61b3e3 | Feiyu Du | 30 July 2014, 18:33:36 UTC | md5 update | 30 July 2014, 18:33:36 UTC |
| 4246703 | Adam Coffman | 30 July 2014, 18:19:10 UTC | make wingspan optional | 30 July 2014, 18:19:10 UTC |
