| 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 |
| 187cbbc | APipe Tester | 02 July 2013, 17:13:22 UTC | Updated class browser cache. | 02 July 2013, 17:13:22 UTC |
| bcc97c4 | Scott Smith | 02 July 2013, 15:42:09 UTC | add "builds" relationship for software results | 02 July 2013, 15:42:09 UTC |
| 54e2433 | Scott Smith | 02 July 2013, 15:41:26 UTC | preliminary COSMIC import | 02 July 2013, 15:41:26 UTC |
| d9e10ad | Eddie Belter | 01 July 2013, 22:51:06 UTC | SomVal: fix known sites in align rreads command | 01 July 2013, 22:52:31 UTC |
| 3a24b9e | Eddie Belter | 01 July 2013, 22:38:02 UTC | InstData GATK: fix metho name in base recalibrator | 01 July 2013, 22:48:36 UTC |
| 68ef14b | Eddie Belter | 26 June 2013, 18:17:04 UTC | InstData Gatk: base recalibrator results use version given | 01 July 2013, 22:48:35 UTC |
| 2386f91 | Eddie Belter | 26 June 2013, 18:16:05 UTC | InstData Gatk: base recalibrator bam result implemented | 01 July 2013, 22:48:35 UTC |
| eed0af9 | Eddie Belter | 26 June 2013, 18:13:53 UTC | InstData Gatk: base recalibrator result adjust kilobytes requested | 01 July 2013, 22:48:34 UTC |
| 4db76a7 | Eddie Belter | 26 June 2013, 17:54:04 UTC | InstData Gatk: base recalibrator result implemented | 01 July 2013, 22:48:34 UTC |
| 492d649 | Eddie Belter | 26 June 2013, 17:42:56 UTC | InstData Gatk: base recalibrator rresult for the output of only the base recalibrator | 01 July 2013, 22:48:33 UTC |
| 534f650 | Eddie Belter | 26 June 2013, 17:41:21 UTC | InstData Gatk: rename base reclibrator result to base recalibrator bam result | 01 July 2013, 22:48:32 UTC |
| 93ac216 | Malachi Griffith | 01 July 2013, 22:16:00 UTC | ClinSeq - update to latest version of cosmic for mutation-diagram plots | 01 July 2013, 22:16:00 UTC |
| 556806b | Thomas Mooney | 01 July 2013, 20:02:18 UTC | Update bacterial blessed build. | 01 July 2013, 20:03:02 UTC |
| 948c14f | Travis Abbott | 01 July 2013, 18:05:56 UTC | bless build 139877037 for somatic variation | 01 July 2013, 18:05:56 UTC |
| 200b089 | Thomas Mooney | 29 June 2013, 23:34:13 UTC | Make sure we operate on the class name and not an object. | 29 June 2013, 23:34:13 UTC |
| f25da58 | apregier | 28 June 2013, 22:23:58 UTC | Update blessed build for gene prediction | 28 June 2013, 22:23:58 UTC |
| 744a4c3 | APipe Tester | 28 June 2013, 22:09:47 UTC | Updated `gmt` tab completion. | 28 June 2013, 22:09:59 UTC |
| e876b81 | APipe Tester | 28 June 2013, 22:08:55 UTC | Updated `genome` tab completion. | 28 June 2013, 22:09:59 UTC |
| 9084033 | APipe Tester | 28 June 2013, 22:07:17 UTC | Updated class browser cache. | 28 June 2013, 22:09:59 UTC |
| 3842b55 | Scott Smith | 28 June 2013, 22:03:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 22:03:30 UTC |
| 8bc25e6 | Scott Smith | 28 June 2013, 22:03:15 UTC | made the CosmicOmim.pm tool compatible with new genome-db-cosmic structure, containing multiple data sets besides the original gene CSV files. | 28 June 2013, 22:03:15 UTC |
| 833b408 | Adam Coffman | 28 June 2013, 21:59:59 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:59:59 UTC |
| b445043 | Adam Coffman | 28 June 2013, 21:59:40 UTC | whitespace | 28 June 2013, 21:59:40 UTC |
| d34b8d8 | Scott Smith | 28 June 2013, 21:53:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:53:10 UTC |
| cd5a629 | Scott Smith | 28 June 2013, 21:52:58 UTC | gmt phred-phrap has a base class, and that module also has a base class. The later was used as the tree delegator, but is being renamed in this commit, with a title befitting its absurdities. | 28 June 2013, 21:52:58 UTC |
| f4cc365 | Scott Smith | 28 June 2013, 21:45:46 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:45:46 UTC |
| 2a2c0c0 | Scott Smith | 28 June 2013, 21:44:33 UTC | bleassed new clinseq build | 28 June 2013, 21:44:33 UTC |
| 212a0d5 | Malachi Griffith | 28 June 2013, 21:35:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:35:10 UTC |
| e1c8fdd | Malachi Griffith | 28 June 2013, 21:34:51 UTC | Fix option to specify no file extension in abi-to-scf | 28 June 2013, 21:34:51 UTC |
| 8df557f | Adam Coffman | 28 June 2013, 21:15:31 UTC | switch explicit lister to genome command crud | 28 June 2013, 21:15:31 UTC |
| d3b9ea9 | Adam Coffman | 28 June 2013, 21:06:05 UTC | add explicit create command | 28 June 2013, 21:06:05 UTC |
| 7345416 | Adam Coffman | 28 June 2013, 20:58:49 UTC | improve cascading delete | 28 June 2013, 20:58:49 UTC |
| cfaf76f | Adam Coffman | 28 June 2013, 20:58:20 UTC | use genome command crud instead of explicit lister | 28 June 2013, 20:58:20 UTC |
| d15e641 | APipe Tester | 28 June 2013, 20:55:34 UTC | updated ur submodule to cd3861c | 28 June 2013, 20:55:34 UTC |
| 2ad85c1 | APipe Tester | 28 June 2013, 19:30:38 UTC | Updated `genome` tab completion. | 28 June 2013, 19:30:38 UTC |
| 986ccdc | APipe Tester | 28 June 2013, 19:28:26 UTC | Updated class browser cache. | 28 June 2013, 19:28:26 UTC |
| ded9691 | Mark Burnett | 28 June 2013, 19:05:27 UTC | use a less fragile test for the GSCApp-RefSeq compatibility test | 28 June 2013, 19:05:27 UTC |
| cda7b97 | Mark Burnett | 28 June 2013, 18:58:22 UTC | fix Define-docs.t expected output for amplicon assembly | 28 June 2013, 18:58:22 UTC |
| 022fde5 | Mark Burnett | 28 June 2013, 17:53:09 UTC | Merge branch 'lims-RefSeq-bug' | 28 June 2013, 17:53:09 UTC |
| 28869f5 | Mark Burnett | 28 June 2013, 17:31:52 UTC | update define docs expected output | 28 June 2013, 17:31:52 UTC |
| b553397 | Eddie Belter | 28 June 2013, 16:29:30 UTC | InstData Import: updates to import SRAs | 28 June 2013, 16:30:05 UTC |
| cd7e2a5 | Eddie Belter | 27 June 2013, 21:45:38 UTC | Sample Manager: do not test sample hash data structure | 28 June 2013, 16:30:04 UTC |
| 4ccaa9f | Eddie Belter | 27 June 2013, 21:44:34 UTC | Sample Manager: store source files as comma delimited string | 28 June 2013, 16:30:04 UTC |
| 94e0e1b | Eddie Belter | 21 June 2013, 19:50:07 UTC | Sample Import Manager: do not display status for build | 28 June 2013, 16:30:04 UTC |
| 8c4deb1 | Eddie Belter | 21 June 2013, 19:31:43 UTC | Sample Import Manager: update status output; fix adding inst data bug | 28 June 2013, 16:30:03 UTC |
| b33f2ed | Eddie Belter | 21 June 2013, 15:29:22 UTC | Sample Import Manager: set job status on sample before make progress and then again when displaying status | 28 June 2013, 16:30:03 UTC |
| 0c64dfd | Eddie Belter | 21 June 2013, 15:24:39 UTC | Sample Import Manager: request build and delete inst data uncommented | 28 June 2013, 16:30:02 UTC |
| b0558f1 | Adam Coffman | 28 June 2013, 16:00:35 UTC | Make AnalysisProject deletions cascade Deleting an analysis project will no longer leave an orphaned configuration set and corresponding allocation. | 28 June 2013, 16:00:35 UTC |
| d1682ad | Adam Coffman | 28 June 2013, 15:59:50 UTC | auto set created_by in the constructor | 28 June 2013, 15:59:50 UTC |
| e37c5cf | Scott Smith | 27 June 2013, 22:22:34 UTC | initial comparison tool examines variant calling results | 27 June 2013, 22:22:34 UTC |
| 3614e51 | Jim Weible | 27 June 2013, 17:52:15 UTC | cleanup | 27 June 2013, 17:52:26 UTC |
| 17668be | Feiyu Du | 27 June 2013, 17:04:41 UTC | approve build diff for som-val, som-var-short and ref-align | 27 June 2013, 17:04:41 UTC |
