| 20ba5d7 | Eddie Belter | 29 July 2015, 23:26:37 UTC | DV2 Novo Realign: bump test dir to v2 | 29 July 2015, 23:26:37 UTC |
| 0bc7a10 | Eddie Belter | 29 July 2015, 23:26:20 UTC | DV2 Novo Realign: use compare_ok | 29 July 2015, 23:26:20 UTC |
| 12d250b | Eddie Belter | 29 July 2015, 23:10:03 UTC | DV2 Novo Realign: use file spec | 29 July 2015, 23:13:26 UTC |
| 68f8af8 | Eddie Belter | 29 July 2015, 23:07:20 UTC | DV2 Novo Realign: remove commented out code | 29 July 2015, 23:07:20 UTC |
| 42554e6 | Eddie Belter | 29 July 2015, 22:59:33 UTC | DV2 Novo Realign: use utility test dir | 29 July 2015, 23:00:42 UTC |
| 27025fe | Eddie Belter | 29 July 2015, 20:46:15 UTC | Merge pull request #886 from ebelter/gm-cc GM Concordance | 29 July 2015, 20:46:15 UTC |
| 0b16aac | Thomas Mooney | 29 July 2015, 18:53:02 UTC | Temporary fix: Load Set type before creating Pool to prevent crash. | 29 July 2015, 18:53:34 UTC |
| 16af5b7 | Thomas Mooney | 29 July 2015, 18:52:46 UTC | Pull in build status determination. | 29 July 2015, 18:52:46 UTC |
| 451b0b5 | Thomas Mooney | 29 July 2015, 18:15:33 UTC | Use an AutoUnloadPool instead of unloading in batches. | 29 July 2015, 18:15:33 UTC |
| c8e9b49 | Thomas Mooney | 29 July 2015, 17:46:47 UTC | Extract a subroutine to generate the model summary. That way we can all generate_model_summary() directly in Perl to get a hash of the data for other use. | 29 July 2015, 17:52:34 UTC |
| cc80ae5 | Thomas Mooney | 29 July 2015, 17:01:19 UTC | Check the model instead of the build. (Some build types don't provide direct access to the PP params.) | 29 July 2015, 17:48:41 UTC |
| d0f386d | Thomas Mooney | 29 July 2015, 17:28:53 UTC | Stop truncating model names. We don't customarily include the PP name in the model name any more, so if it is there it is more useful to know. | 29 July 2015, 17:28:53 UTC |
| 18fdd06 | Thomas Mooney | 29 July 2015, 17:22:47 UTC | Only create closures if we plan to use them. * One is only used one place now, so extract the contents. | 29 July 2015, 17:22:47 UTC |
| 327aaca | Thomas Mooney | 29 July 2015, 17:12:06 UTC | Consolidate actions. | 29 July 2015, 17:12:06 UTC |
| b857579 | Thomas B. Mooney | 29 July 2015, 15:34:21 UTC | Merge pull request #880 from tmooney/dump_flagstats_on_error Dump flagstat data when comparison fails. | 29 July 2015, 15:34:21 UTC |
| b46679b | Thomas B. Mooney | 29 July 2015, 15:33:54 UTC | Merge pull request #892 from tmooney/cleanup_sync_sys_user_with_ldap LDAP Synch: Fix counting bug and cleanup | 29 July 2015, 15:33:54 UTC |
| b6cb0e5 | Allison Penner Regier | 29 July 2015, 15:32:37 UTC | Merge pull request #887 from apregier/bedpe Add the ability to specify a minimum number of hits required | 29 July 2015, 15:32:37 UTC |
| 52ca980 | Thomas Mooney | 29 July 2015, 13:43:38 UTC | Don't try to run LOH without a normal to compare to. | 29 July 2015, 14:14:59 UTC |
| cf0c7b8 | APipe Tester | 29 July 2015, 12:19:21 UTC | Updated `genome` tab completion. | 29 July 2015, 12:19:21 UTC |
| e18cb9a | APipe Tester | 29 July 2015, 12:17:30 UTC | Updated class browser cache. | 29 July 2015, 12:17:30 UTC |
| bc87355 | Eddie Belter | 29 July 2015, 01:43:35 UTC | BedTools: use perl built-in version handling | 29 July 2015, 01:43:35 UTC |
| 1632741 | Eddie Belter | 29 July 2015, 01:42:57 UTC | Genotype Concordance: rm default value for bedtools version, add it to doc as recommended | 29 July 2015, 01:42:57 UTC |
| bd0a93b | Eddie Belter | 28 July 2015, 22:15:43 UTC | Merge pull request #889 from ebelter/rm-iferg RM Refs to iferguso and Related Clean Up | 28 July 2015, 22:15:43 UTC |
| 4b357c2 | Eddie Belter | 28 July 2015, 22:13:44 UTC | Merge pull request #890 from ebelter/rm-downstream-model-props Model: rm downstream models property and useless test | 28 July 2015, 22:13:44 UTC |
| 1a33525 | Thomas B. Mooney | 28 July 2015, 21:54:15 UTC | Merge pull request #884 from iferguson90/errorrate Update BamQC to use packaged bam-errorrate | 28 July 2015, 21:54:15 UTC |
| bd099ec | apregier | 28 July 2015, 21:49:11 UTC | Use error_message | 28 July 2015, 21:49:11 UTC |
| f974a2e | apregier | 28 July 2015, 20:21:30 UTC | Use Genome::Sys->open_file_for_reading instead of IO::File | 28 July 2015, 20:21:30 UTC |
| 90aa684 | apregier | 28 July 2015, 20:18:30 UTC | Refactor: access property from class directly | 28 July 2015, 20:18:30 UTC |
| 7430213 | apregier | 28 July 2015, 20:16:49 UTC | Use perl shortcut for chomping an array | 28 July 2015, 20:16:49 UTC |
| 56d6c1f | apregier | 28 July 2015, 20:15:54 UTC | Check whether output filehandle exists | 28 July 2015, 20:15:54 UTC |
| a653e09 | Thomas B. Mooney | 28 July 2015, 17:39:15 UTC | Merge pull request #879 from tmooney/disconnect_dbh_before_long_waiting_things Disconnect Database Handles before potentially long-running actions | 28 July 2015, 17:39:15 UTC |
| c3125a1 | Thomas B. Mooney | 28 July 2015, 14:46:06 UTC | Merge pull request #865 from tmooney/deduplicate_reference_indices Deduplicate Aligner and Annotation Index Classes | 28 July 2015, 14:46:06 UTC |
| 838ccdb | Jason Walker | 28 July 2015, 14:13:13 UTC | Merge pull request #851 from jasonwalker80/library_duplication_rates Library Duplication Rates from Reference Alignment builds | 28 July 2015, 14:13:13 UTC |
| 76043d8 | Thomas Mooney | 28 July 2015, 14:12:54 UTC | Include a newline in printed message. | 28 July 2015, 14:12:54 UTC |
| 940d4cd | Thomas Mooney | 28 July 2015, 14:12:12 UTC | Refer to correct key when getting counts. | 28 July 2015, 14:12:12 UTC |
| a406746 | Thomas Mooney | 28 July 2015, 14:11:53 UTC | Whitespace. | 28 July 2015, 14:11:53 UTC |
| be673d7 | Thomas Mooney | 28 July 2015, 13:17:46 UTC | Only schedule annotation if we have variants to annotate. | 28 July 2015, 13:17:46 UTC |
| 2079ea5 | Eddie Belter | 27 July 2015, 19:40:52 UTC | Model: rm _model_value from Input | 27 July 2015, 19:40:52 UTC |
| ed245d3 | APipe Tester | 27 July 2015, 18:27:24 UTC | updated jenkins submodule to 6a39f4b | 27 July 2015, 19:22:27 UTC |
| 95bdd7c | Eddie Belter | 27 July 2015, 19:11:06 UTC | BedTools: uncapitalize Version in function name | 27 July 2015, 19:11:12 UTC |
| adb61bc | Eddie Belter | 27 July 2015, 19:01:21 UTC | Model: rm downstream models property and test that did not really test anything | 27 July 2015, 19:01:21 UTC |
| 940b82b | Eddie Belter | 27 July 2015, 18:54:59 UTC | Merge pull request #878 from ebelter/model-rm-trigger-downstream-models Model: remove unused _trigger_downstream_builds | 27 July 2015, 18:54:59 UTC |
| 6993458 | Eddie Belter | 27 July 2015, 18:51:07 UTC | AR Bfast: rm iferguso TODO | 27 July 2015, 18:51:07 UTC |
| ca5205b | Eddie Belter | 27 July 2015, 18:50:02 UTC | AR Mosaik: rm iferguso TODOs | 27 July 2015, 18:50:02 UTC |
| 9b3df87 | Eddie Belter | 27 July 2015, 18:49:16 UTC | AR Crossmatch: remove non-matching command that is never run | 27 July 2015, 18:49:16 UTC |
| 0ac0e26 | Eddie Belter | 27 July 2015, 18:47:11 UTC | AR Crossmatch: remove iferguso comments | 27 July 2015, 18:47:11 UTC |
| 2db6279 | Eddie Belter | 27 July 2015, 18:43:42 UTC | AR Crossmatch: remove fastq file check | 27 July 2015, 18:43:42 UTC |
| afbb7f4 | Eddie Belter | 27 July 2015, 18:40:24 UTC | AR Crossmatch: fix indent | 27 July 2015, 18:40:24 UTC |
| 92ee5f8 | Eddie Belter | 27 July 2015, 18:36:54 UTC | AR BLAT: add 1; | 27 July 2015, 18:36:54 UTC |
| 40353bb | Eddie Belter | 27 July 2015, 18:36:00 UTC | AR BLAT: blast2sam.pl is now packaged | 27 July 2015, 18:36:00 UTC |
| 7c41446 | Eddie Belter | 27 July 2015, 18:35:12 UTC | AR BLAT: rm unneeded comments and commented out code | 27 July 2015, 18:35:12 UTC |
| 2b4c96a | Eddie Belter | 27 July 2015, 18:30:55 UTC | RM Iferguso: remove from under allocated email | 27 July 2015, 18:30:55 UTC |
| 558dfdd | Indraniel Das | 27 July 2015, 17:16:44 UTC | + convert accessor methods into "properties" - this was a github code review recommendation from @tmooney: https://github.com/genome/genome/pull/876/files#r35228345 | 27 July 2015, 17:16:44 UTC |
| ed63e65 | Indraniel Das | 27 July 2015, 16:38:33 UTC | + remove DB::single | 27 July 2015, 16:38:33 UTC |
| ebecd85 | Miranda Fulton | 27 July 2015, 15:25:13 UTC | I removed the temp dir caller | 27 July 2015, 15:25:13 UTC |
| 462694f | Miranda Fulton | 27 July 2015, 15:23:53 UTC | Set up temp directory creation for Sv | 27 July 2015, 15:23:53 UTC |
| 513b692 | Avinash Ramu | 27 July 2015, 15:02:51 UTC | Merge pull request #849 from gatoravi/loh_plot_update Remove unwanted points from LOH plot | 27 July 2015, 15:02:51 UTC |
| 3d18bdc | Thomas Mooney | 27 July 2015, 14:21:09 UTC | IDs could be non-numeric these days. | 27 July 2015, 14:21:09 UTC |
| ba5f374 | Thomas B. Mooney | 27 July 2015, 14:19:17 UTC | Merge pull request #877 from tmooney/fix_microarray_dependent_model_check Fix Microarray dependent model check | 27 July 2015, 14:19:17 UTC |
| ac7459a | Thomas Mooney | 27 July 2015, 14:15:18 UTC | Also disconnect before waiting on PTero workflow. | 27 July 2015, 14:15:18 UTC |
| 2b27910 | Thomas B. Mooney | 27 July 2015, 14:11:09 UTC | Merge pull request #885 from tmooney/workflowbuilder_streamgraph_uses_shellcmd Use shellcmd instead of IPC::Run. | 27 July 2015, 14:11:09 UTC |
| 2c006d8 | APipe Tester | 26 July 2015, 18:51:41 UTC | updated ur submodule to b40400c | 26 July 2015, 18:51:41 UTC |
| 6fa7a43 | APipe Tester | 25 July 2015, 12:17:43 UTC | Updated `genome` tab completion. | 25 July 2015, 12:17:43 UTC |
| aa66c27 | APipe Tester | 25 July 2015, 12:15:43 UTC | Updated class browser cache. | 25 July 2015, 12:15:43 UTC |
| 7e21ab1 | dmorton | 16 June 2015, 18:54:22 UTC | Use WorkflowBuilder to execute InstrumentData::Composite workflow This will allow it to be run via PTero. Eventually the entire programmatic workflow construction process should be done with WorkflowBuilder so that legacy workflow can be retired. | 25 July 2015, 04:08:57 UTC |
| c017835 | David Morton | 25 July 2015, 03:58:49 UTC | Merge pull request #888 from davidlmorton/control_flow PTero: Control flow feature | 25 July 2015, 03:58:49 UTC |
| 59250e1 | dmorton | 24 July 2015, 22:12:16 UTC | Update test data for libptero-perl 0.1.7+ The json representation of a workflow changed with respect to how the links section is encoded. | 24 July 2015, 22:12:16 UTC |
| 533cddb | dmorton | 24 July 2015, 22:06:02 UTC | Update how we build PTero workflows for sdk 0.1.7+ libptero-perl 0.1.7 changed the api related to defining links so that more than one data-flow could be defined between a pair of tasks. | 24 July 2015, 22:06:02 UTC |
| f385e25 | dmorton | 24 July 2015, 22:03:22 UTC | Add test that can be run for Genome::Processes This isn't an automated perl-test but it is a Process that you can run manually. It was useful for making sure Genome::Processes can be run with both legacy workflow as well as PTero without testing using a variant-report or something computationally expensive/complex. | 24 July 2015, 22:05:56 UTC |
| c93dbe3 | Miranda Fulton | 24 July 2015, 18:24:05 UTC | rmoved some junk that didn't need to be there | 24 July 2015, 18:45:48 UTC |
| 66b4934 | Miranda Fulton | 23 July 2015, 21:18:10 UTC | consolidates subroutines | 24 July 2015, 18:45:47 UTC |
| b1d7881 | Miranda Fulton | 23 July 2015, 20:48:15 UTC | Romoved more hardcoded paths and fixed bugs | 24 July 2015, 18:45:46 UTC |
| 799e49a | Miranda Fulton | 23 July 2015, 20:46:46 UTC | Made minor edits to remove some leftover paths | 24 July 2015, 18:45:46 UTC |
| d89eefe | Miranda Fulton | 17 July 2015, 16:27:05 UTC | I updated the test data | 24 July 2015, 18:45:45 UTC |
| 5f74c98 | Miranda Fulton | 17 July 2015, 16:26:21 UTC | modified some of the variables | 24 July 2015, 18:45:45 UTC |
| bffe3f4 | Miranda Fulton | 16 July 2015, 20:11:09 UTC | Started to Fix the VCF date check | 24 July 2015, 18:45:44 UTC |
| af0e409 | Miranda Fulton | 16 July 2015, 17:45:18 UTC | This is the "tumor" bam file in the test | 24 July 2015, 18:45:43 UTC |
| e13968c | Miranda Fulton | 16 July 2015, 17:02:22 UTC | Minor bug fixes and formating | 24 July 2015, 18:45:38 UTC |
| a938bce | Miranda Fulton | 16 July 2015, 16:51:39 UTC | It will now run with a tumor/normal bam pair | 24 July 2015, 18:45:37 UTC |
| 2c7f82c | Miranda Fulton | 07 July 2015, 15:54:23 UTC | Rewrote the test and wrapper | 24 July 2015, 18:45:36 UTC |
| 065f1a7 | Miranda Fulton | 07 July 2015, 14:42:50 UTC | Fixed some errors that were causing problems | 24 July 2015, 18:45:36 UTC |
| 030823b | Miranda Fulton | 06 July 2015, 16:07:59 UTC | Checks all of the test output files | 24 July 2015, 18:45:35 UTC |
| 7ddb0f9 | Miranda Fulton | 06 July 2015, 15:49:48 UTC | wrapper for Speedseq sv | 24 July 2015, 18:45:35 UTC |
| d89fe02 | apregier | 08 July 2015, 15:38:13 UTC | Use error messages when assumptions aren't met | 24 July 2015, 18:15:14 UTC |
| 8ac23f8 | apregier | 08 July 2015, 15:37:34 UTC | Only evaluate min_hit requirements with true positives | 24 July 2015, 18:15:14 UTC |
| 068a99b | apregier | 07 July 2015, 19:26:19 UTC | Optionally include true positives in the json output | 24 July 2015, 18:15:13 UTC |
| 04e577a | apregier | 07 July 2015, 19:03:57 UTC | Move into a subtest | 24 July 2015, 18:15:13 UTC |
| 7820105 | apregier | 07 July 2015, 19:02:38 UTC | Allow min_hit_support and true_positive_file to be passed in the config file | 24 July 2015, 18:15:12 UTC |
| 61b887c | apregier | 07 July 2015, 18:57:46 UTC | Optionally output true positives in a file | 24 July 2015, 18:15:11 UTC |
| 8e4ed2d | apregier | 07 July 2015, 18:34:26 UTC | Add an option to require >1 hit in the gold bedpe to count as true positive | 24 July 2015, 18:15:11 UTC |
| 9290125 | apregier | 07 July 2015, 18:33:48 UTC | Fix order of expected and actual results in is_deeply | 24 July 2015, 18:15:10 UTC |
| a21e99d | Eddie Belter | 23 July 2015, 22:54:54 UTC | GM Conordance: add and use available bed tools versions | 23 July 2015, 22:54:54 UTC |
| 76a1223 | Eddie Belter | 23 July 2015, 22:54:10 UTC | Bed Tools: add latest and available versions | 23 July 2015, 22:54:10 UTC |
| 0594bc1 | Eddie Belter | 23 July 2015, 22:51:54 UTC | GM Conordance: add available picard versions | 23 July 2015, 22:51:54 UTC |
| 99ed1cc | Thomas Mooney | 23 July 2015, 21:45:01 UTC | Use shellcmd instead of IPC::Run | 23 July 2015, 21:45:01 UTC |
| 1dcf781 | Eddie Belter | 23 July 2015, 21:38:49 UTC | Genotype Concordance: add use test | 23 July 2015, 21:38:49 UTC |
| fb80c81 | Ian Ferguson | 23 July 2015, 20:12:02 UTC | Update BamQC to use packaged bam-errorrate | 23 July 2015, 20:12:02 UTC |
| 80e97c0 | Eddie Belter | 23 July 2015, 19:48:57 UTC | Merge pull request #875 from ebelter/model-define Model define.t simplification | 23 July 2015, 19:48:57 UTC |
| 9fa15e8 | David Morton | 23 July 2015, 19:36:34 UTC | Merge pull request #883 from davidlmorton/ptero_sdk_1_6_update Update test-data for Ptero sdk version 0.1.6 | 23 July 2015, 19:36:34 UTC |
| ef18dbd | dmorton | 23 July 2015, 19:34:49 UTC | Update test-data for Ptero sdk version 0.1.6 This version introduced the 'dataFlow' syntax to the link definitions. | 23 July 2015, 19:34:49 UTC |
