| 72bd7fe | Chris Miller | 11 July 2013, 00:22:19 UTC | fixing bed conversion issue | 11 July 2013, 00:22:58 UTC |
| 3c1032c | Scott Smith | 11 July 2013, 00:14:57 UTC | switch to specific subclasses of Genome::Db for clinseq inputs | 11 July 2013, 00:15:09 UTC |
| efc8d54 | Gabriel Sanderson | 10 July 2013, 22:37:58 UTC | Merge branch 'master' into gb_master | 10 July 2013, 22:37:58 UTC |
| bf36cd9 | Gabriel Sanderson | 10 July 2013, 22:37:43 UTC | Since this test uses shellcmd (and should not)... force a use of the module that is being tested so that test tracker can catch failures easier. | 10 July 2013, 22:37:43 UTC |
| a94b24d | Gabriel Sanderson | 10 July 2013, 22:32:07 UTC | Merge branch 'master' into gb_master | 10 July 2013, 22:32:07 UTC |
| 4e821ba | Gabriel Sanderson | 10 July 2013, 22:28:01 UTC | Updated test for new required property | 10 July 2013, 22:30:56 UTC |
| 283cf91 | Feiyu Du | 10 July 2013, 21:41:46 UTC | skip bamqc for imported alignment bam | 10 July 2013, 21:41:46 UTC |
| 1612f25 | Scott Smith | 10 July 2013, 21:22:11 UTC | No longer require a .git subdirectory in a Genome::Db dir, or a "latest" symlink. A meta.yml file is sufficient. | 10 July 2013, 21:22:43 UTC |
| 7a0d6cc | APipe Tester | 10 July 2013, 20:46:53 UTC | Updated `gmt` tab completion. | 10 July 2013, 20:46:53 UTC |
| dd860d9 | APipe Tester | 10 July 2013, 20:45:58 UTC | Updated `genome` tab completion. | 10 July 2013, 20:45:58 UTC |
| f38f394 | APipe Tester | 10 July 2013, 20:43:48 UTC | Updated class browser cache. | 10 July 2013, 20:43:48 UTC |
| b248d55 | Scott Smith | 10 July 2013, 20:31:43 UTC | updated the blessed-build for clinseq: the diff changes when LIMS archives data, and this just occurred | 10 July 2013, 20:32:08 UTC |
| 808c854 | Scott Smith | 10 July 2013, 20:27:51 UTC | ensure that we only fabricate subclasses for things that inherit from Genome::Db | 10 July 2013, 20:32:08 UTC |
| e819329 | Scott Smith | 10 July 2013, 20:24:39 UTC | merge error fix in Genome::Db | 10 July 2013, 20:32:07 UTC |
| a7a889e | APipe Tester | 10 July 2013, 20:25:19 UTC | Updated `gmt` tab completion. | 10 July 2013, 20:25:19 UTC |
| 666055b | APipe Tester | 10 July 2013, 20:24:15 UTC | Updated `genome` tab completion. | 10 July 2013, 20:24:15 UTC |
| 6e30a5b | APipe Tester | 10 July 2013, 20:22:13 UTC | Updated class browser cache. | 10 July 2013, 20:22:13 UTC |
| 64c6193 | Scott Smith | 10 July 2013, 20:15:13 UTC | updated the clinseq pipeline to use Genome::Db entities instead of a hard-coded path to special annotation data | 10 July 2013, 20:15:13 UTC |
| 874aa4d | Scott Smith | 10 July 2013, 20:08:13 UTC | updated to sub-class by source and database | 10 July 2013, 20:08:50 UTC |
| e892650 | APipe Tester | 10 July 2013, 18:54:59 UTC | Updated `gmt` tab completion. | 10 July 2013, 18:54:59 UTC |
| d0c8d53 | APipe Tester | 10 July 2013, 18:53:45 UTC | Updated `genome` tab completion. | 10 July 2013, 18:53:45 UTC |
| 8bbb3b8 | APipe Tester | 10 July 2013, 18:51:33 UTC | Updated class browser cache. | 10 July 2013, 18:51:33 UTC |
| 1eb8bf5 | Feiyu Du | 10 July 2013, 18:26:26 UTC | bug fix | 10 July 2013, 18:26:26 UTC |
| f84b75c | Jason Walker | 10 July 2013, 17:21:46 UTC | Merge t push branch 'master' of ssh://git/srv/git/genome | 10 July 2013, 17:21:46 UTC |
| 8666282 | Jason Walker | 10 July 2013, 17:21:37 UTC | Add PCT_CHIMERAS to the BamQcMetrics summary per refalign build. | 10 July 2013, 17:21:37 UTC |
| eb01eb0 | Dave Larson | 10 July 2013, 03:04:16 UTC | Change workflow command construction to use ref($self) instead of __PACKAGE__ so inheritance does what we want. | 10 July 2013, 03:04:16 UTC |
| 4ee0e24 | APipe Tester | 09 July 2013, 22:07:12 UTC | updated ur submodule to bfb9399 | 09 July 2013, 22:07:12 UTC |
| 93e955a | Chris Miller | 09 July 2013, 21:38:21 UTC | removing depricated tool | 09 July 2013, 21:38:21 UTC |
| 5840552 | Eddie Belter | 09 July 2013, 21:05:07 UTC | SomVal: identify dnp result uses bam_path to get bam from aligned bam result | 09 July 2013, 21:05:07 UTC |
| 2c8f46c | Thomas Mooney | 09 July 2013, 20:47:53 UTC | Don't try to run coverage analysis without an ROI. | 09 July 2013, 20:47:53 UTC |
| 63f4c69 | Thomas Mooney | 09 July 2013, 20:47:13 UTC | Only restrict to target regions if we have an ROI. | 09 July 2013, 20:47:13 UTC |
| ecc6fef | Thomas Mooney | 09 July 2013, 20:46:39 UTC | Change to parent class so we can operate on refined BAMs. | 09 July 2013, 20:46:39 UTC |
| 98c0ac8 | Jason Walker | 09 July 2013, 18:03:37 UTC | A new command line tool to summarize BamQc metrics per build by instrument data. | 09 July 2013, 18:03:37 UTC |
| 6982200 | Eddie Belter | 08 July 2013, 23:00:09 UTC | InstData GATK: base recalibrator uses allocation tmp dir for gatk print reads | 09 July 2013, 17:26:03 UTC |
| c4dfa2f | Eddie Belter | 08 July 2013, 22:51:08 UTC | GMT GATK: add tmp dir option | 09 July 2013, 17:26:03 UTC |
| 9d3f59f | Eddie Belter | 08 July 2013, 21:39:36 UTC | Inst Data Refine Reads Gatk: use indel realigner as bam, source for base recalibrator | 09 July 2013, 17:26:03 UTC |
| 8a0aece | Eddie Belter | 08 July 2013, 20:33:14 UTC | InstData Aligned Bam: add bam_file alias | 09 July 2013, 17:26:02 UTC |
| cdf746e | Eddie Belter | 08 July 2013, 20:27:33 UTC | InstData GATK: add inst data property to base | 09 July 2013, 17:26:02 UTC |
| 9825104 | Eddie Belter | 08 July 2013, 19:43:33 UTC | SomVal: use bam_path instead of merged_alignment_bam_path in align reads | 09 July 2013, 17:26:01 UTC |
| 85eb36c | Eddie Belter | 08 July 2013, 19:42:54 UTC | InstData Aligned Bam Result: rename bam_file to bam_path | 09 July 2013, 17:26:01 UTC |
| f6fdf93 | Eddie Belter | 08 July 2013, 19:09:34 UTC | InstData Merge: create refiner command then call shortcut/execute | 09 July 2013, 17:26:00 UTC |
| 3affef7 | Eddie Belter | 08 July 2013, 19:08:58 UTC | Refine Read GATK: base recalibrator is now base recalibrator bam result | 09 July 2013, 17:26:00 UTC |
| e33b239 | Thomas Mooney | 09 July 2013, 17:17:10 UTC | Can't filter on subclass now that we have an abstract parent class for merged results. | 09 July 2013, 17:17:10 UTC |
| 1a82f57 | Thomas Mooney | 09 July 2013, 16:57:11 UTC | Let apipe-builder clean up other people's builds in "cleanup-succeeded". | 09 July 2013, 16:57:11 UTC |
| 959dc44 | Feiyu Du | 09 July 2013, 15:05:49 UTC | add check to make sure normal and tumor model are not the same | 09 July 2013, 15:05:49 UTC |
| eb4e1de | Thomas Mooney | 09 July 2013, 14:30:33 UTC | Tolerate tabs or other funny spacing in track line. | 09 July 2013, 14:30:33 UTC |
| caa35c7 | Nathan Nutter | 09 July 2013, 01:53:02 UTC | typo | 09 July 2013, 01:53:02 UTC |
| a493d82 | Nathan Nutter | 09 July 2013, 01:44:30 UTC | add methods to walk lineage | 09 July 2013, 01:46:06 UTC |
| a668e7c | Thomas Mooney | 08 July 2013, 21:32:18 UTC | Use parent class so we can run refcov on refined BAMs, too. | 08 July 2013, 21:32:18 UTC |
| 431a3d8 | dmorton | 03 July 2013, 21:04:44 UTC | SoftwareResults generate lock-names more corectly: They will generate the same lock-name whether default params (those with default=undef anyways) are specified or not. | 08 July 2013, 20:46:28 UTC |
| 9535ddf | dmorton | 03 July 2013, 20:47:46 UTC | Added clarifying comment to SoftwareResult.pm | 08 July 2013, 20:46:28 UTC |
| 8758877 | dmorton | 03 July 2013, 19:36:45 UTC | SomaticValidation will not die if no somatic SVs are found to validate | 08 July 2013, 20:46:27 UTC |
| 4afe3bd | Nathan Nutter | 08 July 2013, 15:00:17 UTC | use throws_ok instead of eval | 08 July 2013, 15:00:17 UTC |
| 8b6ab63 | Nathan Nutter | 08 July 2013, 14:54:26 UTC | Merge branch 'RT/91739' CHANGELOG: New sort order in `gmt bed chrom-sort` which is used as the default sorter in DV2. This will correct a sort incompatability between some DV2 results and JoinX. Any existing DV2 results affected by the sort incompatability will need to be set aside. If you get a sort error from JoinX like 'Unsorted data found in stream...' then your DV2 results may be affected. Currently only builds that use GRCh37-lite-+-HPV_Redux-build (116426356) are known to be affected. | 08 July 2013, 14:54:26 UTC |
| 5a0d8af | Nathan Nutter | 05 July 2013, 20:08:32 UTC | use strverssort instead of nsort nsort, from Sort::Naturally, has a different sort preference compared to JoinX which uses GNU strverscmp. | 08 July 2013, 14:05:29 UTC |
| 32b7629 | Nathan Nutter | 05 July 2013, 19:23:15 UTC | add Sort::strverscmp | 08 July 2013, 14:05:29 UTC |
| ea5ed9c | APipe Tester | 06 July 2013, 02:03:57 UTC | updated jenkins submodule to 7d4e5d2 | 06 July 2013, 02:03:57 UTC |
| 8662abb | Nathan Nutter | 05 July 2013, 20:21:11 UTC | rebuilt expected output per Malachi | 05 July 2013, 20:22:08 UTC |
| ed5bb46 | Dave Larson | 05 July 2013, 20:21:16 UTC | point to latest version and docs | 05 July 2013, 20:21:16 UTC |
| 64efeb7 | Malachi Griffith | 05 July 2013, 19:44:16 UTC | ClinSeq - better handling of excluded data | 05 July 2013, 19:44:16 UTC |
| 565ccd0 | Chris Miller | 05 July 2013, 17:27:37 UTC | clarifications in the docs | 05 July 2013, 17:27:52 UTC |
| b9d735c | Nathan Nutter | 05 July 2013, 14:26:51 UTC | updated expected output due to new build run by Obi | 05 July 2013, 14:26:51 UTC |
| 3427f4a | Dave Larson | 03 July 2013, 22:23:55 UTC | update pairoscope submodule to latest version | 03 July 2013, 22:23:55 UTC |
| e878c1a | Dave Larson | 03 July 2013, 21:38:22 UTC | refactor TigraValidationFull and TigraValidation to reduce code duplication | 03 July 2013, 21:38:40 UTC |
| 5a4a265 | Nathan Nutter | 03 July 2013, 20:44:30 UTC | exception message changed | 03 July 2013, 20:44:53 UTC |
| fc5dac4 | Adam Coffman | 03 July 2013, 20:28:49 UTC | escape file names in bed merge command | 03 July 2013, 20:28:49 UTC |
| 0e9ca8a | Scott Smith | 03 July 2013, 20:13:40 UTC | updated apipe-test-clinseq-wer blessed build to 140053444 | 03 July 2013, 20:13:40 UTC |
| 0f48473 | Nathan Nutter | 03 July 2013, 19:17:24 UTC | use compare_ok instead of diff_text_vs_text | 03 July 2013, 20:04:47 UTC |
| bfa82d0 | Nathan Nutter | 03 July 2013, 18:01:28 UTC | whitespace | 03 July 2013, 18:03:26 UTC |
| f8876d0 | Nathan Nutter | 03 July 2013, 18:00:27 UTC | implement a recursive mkdir since make_path is not setting correct group | 03 July 2013, 18:03:25 UTC |
| e5fdff1 | Thomas Mooney | 03 July 2013, 15:46:25 UTC | Don't consider Abandoned builds when deciding what action to take. | 03 July 2013, 15:46:25 UTC |
| 8e52baf | Nathan Nutter | 03 July 2013, 15:39:39 UTC | trivial refactor | 03 July 2013, 15:40:04 UTC |
| 3ecf190 | APipe Tester | 03 July 2013, 15:24:59 UTC | Updated `gmt` tab completion. | 03 July 2013, 15:24:59 UTC |
| fd642e3 | APipe Tester | 03 July 2013, 15:23:58 UTC | Updated `genome` tab completion. | 03 July 2013, 15:23:58 UTC |
| 7ab0c53 | APipe Tester | 03 July 2013, 15:21:36 UTC | Updated class browser cache. | 03 July 2013, 15:21:36 UTC |
| 268cfe3 | Adam Coffman | 03 July 2013, 14:45:00 UTC | have shorter analysis-project command names | 03 July 2013, 14:45:00 UTC |
| d0e79ef | Nathan Nutter | 03 July 2013, 14:35:35 UTC | refactor: rename paramater | 03 July 2013, 14:35:58 UTC |
| 7305880 | Nathan Nutter | 03 July 2013, 14:33:15 UTC | use Params::Validate instead of reinventing | 03 July 2013, 14:35:57 UTC |
| 9ba1403 | Dave Larson | 03 July 2013, 13:45:09 UTC | Our SV pipeline contains a number of places where output is restricted to chromosomes 1-22, X, Y and MT. Obviously, this is not always desirable as all of our sequencing is not human and we occasionally have "extra" chromosomes that need to be included because we are looking for viruses. This commit does a few things: * Adds a DV2 filter called TigraValidationFull that attempts to run on any chromosomes in the fasta .fai file. There are probably better ways to find those chromosomes (examining the BAM header), but these changes were quick and aimed at addressing a current analysis project. This TigraValidationFull filter is needed to interact with BreakdancerMax that Scott recently committed to remove similar restrictions in BreakDancer's DV2 module. * Adds and option to G::M::T::BreakDancer::SplitFiles so that it optionally doesn't split its files by this same hardcoded chromosome list. TigraValidationFull uses this option to pick up the extra chromosomes. * Note that the test for TigraValidationFull is just a copy of the tests for the regular TigraValidation. Coverage of the new functionality is not included and is deferred for later. | 03 July 2013, 13:51:49 UTC |
| 362be71 | Chris Miller | 03 July 2013, 13:50:13 UTC | tar fix | 03 July 2013, 13:50:45 UTC |
| a166535 | Thomas Mooney | 03 July 2013, 13:13:20 UTC | Remove shortcut hack to Pindel workflow. The flow project will be out soon, at which point this no longer has utility. With the recent addition of indel normalization, this is consuming too much memory in the workflow server job, so remove it early. | 03 July 2013, 13:13:20 UTC |
| 658e0fc | Travis Abbott | 02 July 2013, 22:47:19 UTC | add VcfAnnotationStrategy modele for phenotype correlation | 02 July 2013, 22:47:19 UTC |
| 8008d13 | APipe Tester | 02 July 2013, 22:05:31 UTC | updated ur submodule to f34959a | 02 July 2013, 22:05:31 UTC |
| a30b161 | Anthony Brummett | 02 July 2013, 20:53:50 UTC | Localize the variable to a smaller scope | 02 July 2013, 21:50:59 UTC |
| 51818bd | Anthony Brummett | 02 July 2013, 20:47:05 UTC | Be more precise when copying properties for on-the-fly classes Instead of copying _all_ properties from the template class, or by-hand excluding UR::Object::id, explicitly include only properties starting at a specific point in the hierarchy | 02 July 2013, 21:50:58 UTC |
| 2085c59 | Scott Smith | 02 July 2013, 21:47:28 UTC | fixed CreateCrossSampleVcf.t to use /tmp/ for tmpdirs and to auto-cleanup | 02 July 2013, 21:47:28 UTC |
| 6375f77 | Scott Smith | 02 July 2013, 21:22:52 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 July 2013, 21:22:52 UTC |
| 30ddb2d | Scott Smith | 02 July 2013, 21:22:42 UTC | made input variant lists use a more specific data type for somatic validation models | 02 July 2013, 21:22:42 UTC |
| 28c1909 | Nathan Nutter | 01 July 2013, 19:06:09 UTC | add debug code to catch cross-device renaming issue | 02 July 2013, 19:38:01 UTC |
| a6dc723 | Nathan Nutter | 01 July 2013, 18:46:17 UTC | add Genome::Sys::retry | 02 July 2013, 19:38:00 UTC |
| dd8162f | Nathan Nutter | 01 July 2013, 18:45:11 UTC | add named_args | 02 July 2013, 19:38:00 UTC |
| 48a1ac4 | Nathan Nutter | 01 July 2013, 20:25:48 UTC | add explicit check for an undefined locusdir | 02 July 2013, 19:21:10 UTC |
| b581951 | Nathan Nutter | 01 July 2013, 18:45:45 UTC | whitespace | 02 July 2013, 19:21:09 UTC |
| 940328e | APipe Tester | 02 July 2013, 19:05:27 UTC | Updated `genome` tab completion. | 02 July 2013, 19:05:27 UTC |
| 87d10b5 | APipe Tester | 02 July 2013, 19:03:45 UTC | Updated class browser cache. | 02 July 2013, 19:03:45 UTC |
| 5fbb77f | Scott Smith | 02 July 2013, 18:53:06 UTC | updated somatic-variation compare variants comments | 02 July 2013, 18:53:06 UTC |
| 27d4625 | Scott Smith | 02 July 2013, 18:47:43 UTC | Genome::Command::Tester from the old clinseq tester module. This module exports the run_and_diff() function. Now updated to get test the class name matching the test name by default. In this case, or when a class name is specified instead of a full command, it runs the help_synopsis(), replacing /tmp/output_dir with the desired output directory. | 02 July 2013, 18:47:43 UTC |
| 877d58f | Scott Smith | 02 July 2013, 18:36:02 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 July 2013, 18:36:02 UTC |
| 9cbcf8b | Scott Smith | 02 July 2013, 18:34:08 UTC | initial build comparison module for somatic variants | 02 July 2013, 18:34:08 UTC |
| 2a927be | APipe Tester | 02 July 2013, 17:15:42 UTC | Updated `genome` tab completion. | 02 July 2013, 17:15:42 UTC |
