| 814d905 | Mark Burnett | 22 September 2014, 15:08:50 UTC | Merge pull request #45 from nnutter/master _reload_allocation also gets called after allocations are deleted | 22 September 2014, 15:08:50 UTC |
| 590adfc | Mark Burnett | 22 September 2014, 15:04:29 UTC | Merge pull request #48 from mark-burnett/remove-bio-db-fasta Delete G:M:T:BioDbFasta* | 22 September 2014, 15:04:29 UTC |
| d1e3159 | Mark Burnett | 22 September 2014, 14:56:59 UTC | Merge pull request #42 from mark-burnett/fix-bam-readcount-header-skipping Skip possible header lines less aggressively in G:M:T:A:Coverage:BamReadcount | 22 September 2014, 14:56:59 UTC |
| 7922dfc | Mark Burnett | 22 September 2014, 14:49:29 UTC | delete G:M:T:BioDbFasta* | 22 September 2014, 14:49:29 UTC |
| 3c75f8b | Mark Burnett | 22 September 2014, 14:46:01 UTC | gmt a cov add- & bam-readcount: fix header regexes | 22 September 2014, 14:46:01 UTC |
| e7e2ae8 | Susanna Siebert | 22 September 2014, 14:22:53 UTC | Merge pull request #37 from susannasiebert/cle_legend_file Create a legend file for CLE reports | 22 September 2014, 14:22:53 UTC |
| ccb366f | Mark Burnett | 22 September 2014, 13:15:55 UTC | Merge pull request #44 from mark-burnett/fix-cleanup-archive-directory Fix G:D:A _cleanup_archive_directory | 22 September 2014, 13:15:55 UTC |
| 136be01 | Mark Burnett | 22 September 2014, 13:15:18 UTC | Merge pull request #39 from mark-burnett/delete-archived-allocation Allow archived disk allocations to be deleted directly from tape | 22 September 2014, 13:15:18 UTC |
| 906ad1b | APipe Tester | 20 September 2014, 12:15:20 UTC | Updated `genome` tab completion. | 20 September 2014, 12:15:20 UTC |
| c6db398 | APipe Tester | 20 September 2014, 12:13:49 UTC | Updated class browser cache. | 20 September 2014, 12:13:49 UTC |
| 4d92317 | Nathaniel Nutter | 20 September 2014, 04:34:23 UTC | _reload_allocation also gets called after allocations are deleted | 20 September 2014, 04:34:23 UTC |
| 3ce2000 | Mark Burnett | 19 September 2014, 20:34:47 UTC | D:A notify of failure when `rm` from tape fails | 19 September 2014, 20:34:47 UTC |
| 469335e | Mark Burnett | 19 September 2014, 20:33:11 UTC | D:A bugfix - test whether $directory is a dir `-a` seems to test whether it's a file or directory, which does not seem to be the intent. | 19 September 2014, 20:33:11 UTC |
| 85f1899 | Mark Burnett | 19 September 2014, 20:32:57 UTC | D:A bugfix - invalid test syntax | 19 September 2014, 20:32:57 UTC |
| 90cbb92 | Susanna Siebert | 19 September 2014, 18:50:58 UTC | Encode the list of filters to be excluded from the legend file in a more generic way | 19 September 2014, 18:50:58 UTC |
| ae449bb | Susanna Siebert | 19 September 2014, 18:37:42 UTC | Bugfix: Legend file name needs to be unique When there are multiple reports in a plan file they will be written to the same directory. The legend files are unique to a report. With the old naming scheme the legend file names would clash if there were more than one. Now they're being created uniquely by using each report's name. | 19 September 2014, 18:37:42 UTC |
| 07fbad7 | Jason Walker | 19 September 2014, 17:48:03 UTC | Add the homopolymer filter/expert to the somatic indel report. | 19 September 2014, 17:48:03 UTC |
| 3f494de | Jason Walker | 19 September 2014, 17:31:05 UTC | Separate commands for gold evaluations. Also consolidate the germline/somatic wrappers into a ModelReport command. This time with the new wrappers added. | 19 September 2014, 17:31:05 UTC |
| a55054c | Jason Walker | 19 September 2014, 16:40:52 UTC | Separate commands for gold evaluations. Also consolidate the germline/somatic wrappers into a ModelReport command. | 19 September 2014, 16:40:52 UTC |
| a02ed2b | Mark Burnett | 19 September 2014, 15:28:55 UTC | gmt a cov bam-readcount - only check for header on first line | 19 September 2014, 15:28:55 UTC |
| dc5a0a3 | Mark Burnett | 19 September 2014, 15:26:57 UTC | gmt a cov bam-readcount - use same header regex as AddReadcounts | 19 September 2014, 15:26:57 UTC |
| 92348ac | Mark Burnett | 19 September 2014, 15:24:55 UTC | gmt a cov add-readcounts - simplify header regex | 19 September 2014, 15:24:55 UTC |
| 1ce2c94 | Jim Weible | 19 September 2014, 14:56:33 UTC | Merge pull request #41 from jweible/master Remove check for useless, deleted default database | 19 September 2014, 14:56:33 UTC |
| 1cd240b | Jim Weible | 19 September 2014, 13:04:23 UTC | Remove check for useless, deleted default database Despite evidence to the contrary, the user claims this is still in use. Remove the offending line in the test that references data she claims is not in use so that tests pass. | 19 September 2014, 13:04:23 UTC |
| 0c59396 | apregier | 18 September 2014, 22:10:40 UTC | Merge pull request #35 from apregier/indel_position Correctly report coordinates and alleles for indels | 18 September 2014, 22:10:40 UTC |
| 832c3b4 | apregier | 18 September 2014, 22:02:14 UTC | Move utility methods to G::Utility::Vcf | 18 September 2014, 22:02:14 UTC |
| f493588 | Mark Burnett | 18 September 2014, 21:33:18 UTC | D:A extract get_deletion_observers | 18 September 2014, 21:35:11 UTC |
| 0055b1b | Mark Burnett | 18 September 2014, 21:28:52 UTC | D:A move duplicate lines out of if/else | 18 September 2014, 21:28:52 UTC |
| e0e2a37 | Mark Burnett | 18 September 2014, 21:28:05 UTC | D:A delete archive inside commit observer | 18 September 2014, 21:28:05 UTC |
| a23ca5f | Mark Burnett | 18 September 2014, 21:18:00 UTC | whitespace | 18 September 2014, 21:18:00 UTC |
| 3bac170 | Mark Burnett | 18 September 2014, 21:17:21 UTC | D:A delete timeline events when deleting archived allocation | 18 September 2014, 21:17:21 UTC |
| 36c71d6 | Mark Burnett | 18 September 2014, 21:16:54 UTC | D:A extract _delete_timeline_events | 18 September 2014, 21:16:54 UTC |
| 1bb552a | Mark Burnett | 18 September 2014, 21:05:27 UTC | D:Allocation directly delete archived allocations | 18 September 2014, 21:05:27 UTC |
| 787a0e4 | apregier | 18 September 2014, 20:34:03 UTC | Make condition clearer | 18 September 2014, 20:34:03 UTC |
| a039f0d | apregier | 18 September 2014, 19:33:43 UTC | Use coordinate converter to get correct indel positions | 18 September 2014, 19:33:43 UTC |
| b892188 | apregier | 18 September 2014, 19:33:20 UTC | Update test so offset insertion is unambiguous | 18 September 2014, 19:33:20 UTC |
| 4d8fbc3 | Susanna Siebert | 18 September 2014, 19:16:19 UTC | make tests pass | 18 September 2014, 19:21:43 UTC |
| 17df87e | Susanna Siebert | 18 September 2014, 15:53:27 UTC | Field descriptions for interpreters | 18 September 2014, 19:21:42 UTC |
| 1b8b6fb | Susanna Siebert | 18 September 2014, 14:27:05 UTC | Framework for writing a legend file | 18 September 2014, 19:21:42 UTC |
| 68c2701 | Thomas B. Mooney | 18 September 2014, 19:15:38 UTC | Merge pull request #33 from tmooney/software_result_test_name_collision Reload the owner after taking action on a disk allocation. | 18 September 2014, 19:15:38 UTC |
| 13b432a | apregier | 18 September 2014, 18:45:15 UTC | Refactor - move coordinate converting code to a utility class | 18 September 2014, 18:45:54 UTC |
| b4d49f4 | Michael J. Kiwala | 18 September 2014, 17:23:45 UTC | update blessed gene-prediction-bacterial build | 18 September 2014, 17:24:48 UTC |
| c510c56 | Dave Larson | 18 September 2014, 02:08:55 UTC | additional, more complex test cases | 18 September 2014, 02:08:55 UTC |
| b8e3a01 | Dave Larson | 17 September 2014, 21:41:44 UTC | update coordinates for the deletion test case. Add notes | 17 September 2014, 21:41:44 UTC |
| d684329 | Thomas Mooney | 17 September 2014, 21:39:31 UTC | Remove unneeded variable. | 17 September 2014, 21:39:31 UTC |
| bda007c | Thomas Mooney | 17 September 2014, 21:37:51 UTC | Whitespace. | 17 September 2014, 21:37:51 UTC |
| 503c44c | Thomas Mooney | 17 September 2014, 21:30:37 UTC | Reload owner when reloading allocation. Multiple alignment actions update their owners in the spawned process, so promptly load the changes to either trigger immediate notification of conflicts or prevent future changes from causing them. | 17 September 2014, 21:30:37 UTC |
| a604391 | Thomas B. Mooney | 17 September 2014, 21:05:07 UTC | Merge pull request #34 from tmooney/subject_mapping_tags Ability to Tag Subject Mappings | 17 September 2014, 21:05:07 UTC |
| edb8b70 | Thomas Mooney | 17 September 2014, 20:55:54 UTC | Tag the deploy of the new bridge table. | 17 September 2014, 20:55:54 UTC |
| 2b4bf0a | Mark Burnett | 17 September 2014, 18:57:06 UTC | fix GenePrediction::Bacterial file diff message | 17 September 2014, 19:27:15 UTC |
| 167e7b0 | Thomas B. Mooney | 17 September 2014, 19:09:35 UTC | Merge pull request #32 from tmooney/process_somvar_use_input_builds Use input builds in ProcessVariation command | 17 September 2014, 19:09:35 UTC |
| de61eef | apregier | 17 September 2014, 17:53:45 UTC | Correctly report coordinates and alleles for indels | 17 September 2014, 17:53:45 UTC |
| 60c0b16 | apregier | 17 September 2014, 17:52:09 UTC | Merge pull request #31 from apregier/caf_bugfix Caf bugfix | 17 September 2014, 17:52:09 UTC |
| f305dfd | Adam Coffman | 17 September 2014, 17:51:27 UTC | Merge pull request #30 from acoffman/fix_datatype Correct data type in ObjectWithCreatedBy | 17 September 2014, 17:51:27 UTC |
| 6a3ec30 | Mark Burnett | 17 September 2014, 17:17:33 UTC | Merge pull request #28 from mark-burnett/refactor-ap-config Report missing/not-yet-created models for InstrumentData in genome analysis-project config-for-instrument-data | 17 September 2014, 17:17:33 UTC |
| 89ef5f2 | dufeiyu | 17 September 2014, 17:11:18 UTC | Merge pull request #24 from dufeiyu/homp Add Variant-Reporting homopolymer expert/filter | 17 September 2014, 17:11:18 UTC |
| 73a785a | Feiyu Du | 17 September 2014, 16:56:51 UTC | create VcfHomopolymerReporter to handle homopolymer report | 17 September 2014, 16:56:51 UTC |
| 3dfd532 | apregier | 17 September 2014, 15:02:53 UTC | Don't test multiple versions of CAF The multiple versions of CAF are exercised in the DbsnpAfParser, so we don't need to combinatorially test all of them in this class which uses the parser. We can just test the new one. | 17 September 2014, 15:02:53 UTC |
| 8442268 | Mark Burnett | 17 September 2014, 14:34:17 UTC | G:C:Profile:Item has_model_for uses a UR set | 17 September 2014, 14:34:17 UTC |
| 82168f6 | Feiyu Du | 17 September 2014, 01:06:58 UTC | add homopolymer to VcfReport, vcf portion of indel plan file, and snv plan file | 17 September 2014, 01:06:58 UTC |
| 0dfa52a | Eddie Belter | 16 September 2014, 22:52:18 UTC | InstData Import: improve finding of instdata by og data path and downsample ratio | 16 September 2014, 22:52:34 UTC |
| d716e99 | Eddie Belter | 16 September 2014, 22:51:34 UTC | InstData Import: compare downsample ratio w/ == in helpers | 16 September 2014, 22:52:33 UTC |
| 71459c4 | Eddie Belter | 16 September 2014, 22:51:03 UTC | InstData Import: test downsample ratio is set in test | 16 September 2014, 22:52:33 UTC |
| 9d38436 | Thomas Mooney | 16 September 2014, 20:39:10 UTC | Test for bridge between tags and subject mappings. | 16 September 2014, 20:41:55 UTC |
| 04c5b09 | Thomas Mooney | 16 September 2014, 20:21:01 UTC | Accessors for tags/subject-mappings (via bridge entities). | 16 September 2014, 20:41:49 UTC |
| d417cdd | Thomas Mooney | 16 September 2014, 20:20:30 UTC | New class for tag/subject-mapping bridge. | 16 September 2014, 20:41:49 UTC |
| d95347b | Thomas Mooney | 16 September 2014, 20:23:10 UTC | Database table to bridge tags and subject mappings. | 16 September 2014, 20:41:49 UTC |
| 44593db | Thomas Mooney | 16 September 2014, 19:33:23 UTC | Reload ourselves after purging disk allocation. The purge process may set a test_name on the object in which case the lookup_hash will have been modified. To avoid concurrent modification reload the object before setting our desired test_name. | 16 September 2014, 19:45:38 UTC |
| 8aae333 | Thomas Mooney | 16 September 2014, 18:57:04 UTC | Whitespace | 16 September 2014, 19:06:12 UTC |
| 12ba352 | Thomas Mooney | 16 September 2014, 18:52:44 UTC | Eliminate redundant query for reference build. | 16 September 2014, 19:05:14 UTC |
| 56dcdec | Thomas Mooney | 16 September 2014, 18:51:23 UTC | Use the input builds associated with our builds. | 16 September 2014, 19:04:12 UTC |
| dc1dd15 | Travis Abbott | 16 September 2014, 18:55:15 UTC | fix numeric vs string eq for ids looks like genome model build abandon-failed never got updated for the switch from numeric to uuid database ids. | 16 September 2014, 18:55:15 UTC |
| d847f90 | Feiyu Du | 16 September 2014, 18:21:02 UTC | typo and doc fix in response to code review | 16 September 2014, 18:21:02 UTC |
| 79f7472 | Mark Burnett | 16 September 2014, 18:13:48 UTC | G:C:AP:C:ConfigForInstrumentData update missing model message | 16 September 2014, 18:13:48 UTC |
| 2dac5fe | Feiyu Du | 16 September 2014, 17:20:11 UTC | 1. Add homopolymer expert/filter to plan and resource 2. add joinx_version error to homopolymer adaptor | 16 September 2014, 17:20:11 UTC |
| 7422f61 | apregier | 16 September 2014, 16:18:04 UTC | Use constant TAG | 16 September 2014, 16:18:04 UTC |
| b6e5a5a | apregier | 16 September 2014, 16:05:43 UTC | Bugfix for CAF interpreter The Caf interpreter test was not actually testing the new Number=R caf field. Updated the tests to actually test this,which broke. Fixed how we were calling info_for_allele to return the expected value. | 16 September 2014, 16:09:31 UTC |
| 52efcb5 | Adam Coffman | 16 September 2014, 15:59:39 UTC | clean up test case | 16 September 2014, 15:59:39 UTC |
| 7f1966c | mkiwala | 16 September 2014, 15:50:49 UTC | Merge pull request #29 from mkiwala/update-datatype-of-featurelist-subject-id Make datatype of subject_id match between db and G::FeatureList | 16 September 2014, 15:50:49 UTC |
| 33e4c9e | Adam Coffman | 16 September 2014, 15:44:09 UTC | correct data type of created_by | 16 September 2014, 15:44:09 UTC |
| d0c76ea | Michael J. Kiwala | 16 September 2014, 15:18:27 UTC | Make datatype of subject_id match between db and G::FeatureList | 16 September 2014, 15:18:27 UTC |
| 63ed8fa | apregier | 16 September 2014, 14:45:10 UTC | Merge pull request #23 from apregier/trio_workflow Trio workflow | 16 September 2014, 14:45:10 UTC |
| 7e5d731 | Mark Burnett | 16 September 2014, 13:52:02 UTC | G:C:AP:C:ConfigForInstrumentData reports missing models | 16 September 2014, 14:10:05 UTC |
| 6d28b23 | Mark Burnett | 16 September 2014, 13:18:49 UTC | G:C:RuleModelMap extract new match method | 16 September 2014, 13:19:35 UTC |
| 0c8f1bd | Mark Burnett | 16 September 2014, 13:15:13 UTC | G:C:RuleModelMap rename match to match_and_concretize | 16 September 2014, 13:19:29 UTC |
| 45f72ee | APipe Tester | 16 September 2014, 12:18:06 UTC | Updated `genome` tab completion. | 16 September 2014, 12:18:06 UTC |
| 167ba3d | APipe Tester | 16 September 2014, 12:16:05 UTC | Updated class browser cache. | 16 September 2014, 12:16:05 UTC |
| ad6cdd5 | Jason Walker | 15 September 2014, 21:19:34 UTC | optional params to pass VCF files for indels and snvs rather than use the model DV2 VCF file. | 15 September 2014, 21:19:34 UTC |
| 7764055 | Jason Walker | 15 September 2014, 21:16:56 UTC | Use GffReader instead of natively parsing GFF/GTF entries. | 15 September 2014, 21:16:56 UTC |
| 5b2cccd | Susanna Siebert | 15 September 2014, 20:57:40 UTC | Merge pull request #25 from susannasiebert/vcf_header Write vcf header meta info arrays as separate lines | 15 September 2014, 20:57:40 UTC |
| 9d253d4 | Thomas B. Mooney | 15 September 2014, 20:56:01 UTC | Merge pull request #22 from tmooney/tag_crud_commands Update and Lister commands for Tags | 15 September 2014, 20:56:01 UTC |
| 27584f1 | APipe Tester | 15 September 2014, 19:52:29 UTC | updated jenkins submodule to 91e07fb | 15 September 2014, 20:29:37 UTC |
| 485efdf | APipe Tester | 15 September 2014, 19:52:08 UTC | updated ur submodule to bbe110a | 15 September 2014, 20:29:36 UTC |
| 61dd49f | Eddie Belter | 15 September 2014, 19:56:07 UTC | Merge pull request #21 from ebelter/downsample Downsample | 15 September 2014, 19:56:07 UTC |
| c731e64 | Feiyu Du | 15 September 2014, 19:41:40 UTC | bug fix and code improvement from code review | 15 September 2014, 19:41:40 UTC |
| 1b35bde | Eddie Belter | 15 September 2014, 19:20:57 UTC | Merge branch 'downsample' of github.com:ebelter/genome into downsample | 15 September 2014, 19:20:57 UTC |
| d292041 | Eddie Belter | 15 September 2014, 19:18:50 UTC | InstData Import: fix misspelling | 15 September 2014, 19:18:50 UTC |
| 94d6c3c | Travis Abbott | 11 September 2014, 15:09:37 UTC | add G:F:Breakdancer::ToBedPe to convert breakdancer entries to bedpe. | 15 September 2014, 18:13:46 UTC |
| 978a57b | Travis Abbott | 11 September 2014, 15:09:06 UTC | add lib_read_count method to breakdancer entry object returns the number of reads originating from the given library | 15 September 2014, 18:13:46 UTC |
| 4dcd663 | Travis Abbott | 11 September 2014, 15:04:29 UTC | add custom_by_name method to bedpe object my $idx = $entry->{header}->custom_field_index("foo"); $entry->{custom}[$idx]; is now $entry->custom_by_name("foo"); | 15 September 2014, 18:13:45 UTC |
