| 08881c0 | Eddie Belter | 11 April 2016, 22:43:59 UTC | Save to file uses config_to_yaml; remove white space in expected output | 11 April 2016, 22:43:59 UTC |
| 83bcc4b | Eddie Belter | 09 April 2016, 00:39:48 UTC | Merge pull request #1 from tmooney/qc-config-cmds Quick test for the new QC config diff command. | 09 April 2016, 00:39:48 UTC |
| b17fe7e | Thomas Mooney | 07 April 2016, 22:20:25 UTC | Quick test of the QC config diff command. | 07 April 2016, 22:20:25 UTC |
| 12eeabb | Eddie Belter | 07 April 2016, 21:41:35 UTC | QC Config has a simple diff command | 07 April 2016, 21:41:35 UTC |
| d4d35d6 | Eddie Belter | 07 April 2016, 21:41:05 UTC | QC Config has a view command | 07 April 2016, 21:41:05 UTC |
| 4a175a8 | Eddie Belter | 07 April 2016, 21:31:40 UTC | QC Config has config_to_yaml | 07 April 2016, 21:31:40 UTC |
| 58fe0cd | Eddie Belter | 07 April 2016, 21:29:22 UTC | QC Config has __display_name__ | 07 April 2016, 21:29:22 UTC |
| 926809c | Thomas B. Mooney | 07 April 2016, 20:18:41 UTC | Merge pull request #1333 from tmooney/remove_old_modelgroup_commands Remove old ModelGroup commands. | 07 April 2016, 20:18:41 UTC |
| 5076938 | APipe Tester | 07 April 2016, 18:18:57 UTC | updated graphite submodule to 00710ee | 07 April 2016, 19:28:34 UTC |
| 23a8afb | APipe Tester | 07 April 2016, 18:18:49 UTC | updated jenkins submodule to f5af37b | 07 April 2016, 19:28:33 UTC |
| 3863a1f | Jason Walker | 07 April 2016, 19:16:34 UTC | Merge pull request #1322 from jasonwalker80/true_csv_support True CSV parsing support. | 07 April 2016, 19:16:34 UTC |
| 94b6fa0 | Thomas B. Mooney | 07 April 2016, 18:37:32 UTC | Merge pull request #1312 from tmooney/heartbeat_check_for_ptero Support Heartbeat Check for PTero-based Builds. | 07 April 2016, 18:37:32 UTC |
| f4f9c91 | Dan Koboldt | 07 April 2016, 15:43:18 UTC | New module for running germline SNP/indel calling in parallel | 07 April 2016, 15:43:18 UTC |
| abbeec7 | Dan Koboldt | 07 April 2016, 15:42:50 UTC | Allowed manual provision of data ratio | 07 April 2016, 15:42:50 UTC |
| a9917c4 | Eddie Belter | 31 March 2016, 19:43:24 UTC | Merge pull request #1330 from ebelter/instdata-import-sanitize InstData Import: Merge and Modify Sanitize and Split Bam | 31 March 2016, 19:43:24 UTC |
| ff3402d | Eddie Belter | 30 March 2016, 21:01:09 UTC | SanAndSplit Bam: PR updates | 30 March 2016, 21:01:09 UTC |
| efda77f | Thomas Mooney | 30 March 2016, 20:03:06 UTC | Remove old model-group commands. | 30 March 2016, 20:03:06 UTC |
| 68df760 | Thomas B. Mooney | 30 March 2016, 18:35:41 UTC | Merge pull request #1329 from tmooney/fix_else_cases_for_1316 PteroWorkflowMixin: Pass correct number of parameters in the "else" cases as well. | 30 March 2016, 18:35:41 UTC |
| 53c13e0 | Feiyu Du | 30 March 2016, 18:14:50 UTC | Merge pull request #1331 from dufeiyu/update_trio Update blessed process object for Jenkins genome-process-test | 30 March 2016, 18:14:50 UTC |
| 7fa8730 | Feiyu Du | 30 March 2016, 17:31:54 UTC | update with new process | 30 March 2016, 17:31:54 UTC |
| 9af80de | Thomas B. Mooney | 30 March 2016, 14:27:23 UTC | Merge pull request #1327 from tmooney/determine_error_checks_one_more_line_properly DetermineError: Properly handle case where dies on next line of logs. | 30 March 2016, 14:27:23 UTC |
| fac6b12 | Eddie Belter | 29 March 2016, 21:56:17 UTC | Update tests and data | 29 March 2016, 21:56:17 UTC |
| 78c7beb | Feiyu Du | 29 March 2016, 21:44:41 UTC | Merge pull request #1323 from dufeiyu/c_position Add c_position to variant report | 29 March 2016, 21:44:41 UTC |
| 04f2016 | Thomas Mooney | 29 March 2016, 21:01:45 UTC | Need to add a blank parameter in the "else" cases as well. This corrects an omission from #1316. | 29 March 2016, 21:02:08 UTC |
| 6b05eeb | APipe Tester | 29 March 2016, 20:32:41 UTC | updated graphite submodule to 91c31cf | 29 March 2016, 20:32:41 UTC |
| 9ff7d47 | Thomas B. Mooney | 29 March 2016, 18:54:24 UTC | Merge pull request #1316 from tmooney/ptero_workflow_output_includes_id Add an ID column to the Ptero Workflow display. | 29 March 2016, 18:54:24 UTC |
| a93dacc | Eddie Belter | 29 March 2016, 18:52:02 UTC | Switch to picard sort so picard downsample does not fail | 29 March 2016, 18:52:10 UTC |
| d62c70e | Thomas B. Mooney | 29 March 2016, 17:55:15 UTC | Merge pull request #1306 from tmooney/use_job_group_with_ptero Specify a default job group for PTero-launched jobs. | 29 March 2016, 17:55:15 UTC |
| c9f9c5c | Thomas Mooney | 29 March 2016, 14:24:39 UTC | Carry over no-PID status from #1287. | 29 March 2016, 14:24:39 UTC |
| 1664bdb | Thomas Mooney | 17 March 2016, 20:37:43 UTC | Really get all the executions. get_all_executions doesn't! | 29 March 2016, 14:23:42 UTC |
| 4f18547 | Thomas Mooney | 16 March 2016, 14:40:28 UTC | Support Heartbeat Check for Ptero-based Builds. | 29 March 2016, 14:23:42 UTC |
| 4d6e42a | Thomas B. Mooney | 29 March 2016, 14:16:48 UTC | Merge pull request #1287 from tmooney/heartbeatcheck_missing_pids_isnt_fatal Don't die in HeartbeatCheck if no PIDs Found. | 29 March 2016, 14:16:48 UTC |
| 29781f6 | Thomas Mooney | 28 March 2016, 22:50:34 UTC | Need to check the one more line in the next iteration. Otherwise we're really checking the same line a second time, which doesn't get us any additional information. | 28 March 2016, 22:57:12 UTC |
| a07cb35 | Eddie Belter | 25 March 2016, 23:08:56 UTC | SanAndSplit: update tests and convert to subtests | 25 March 2016, 23:27:18 UTC |
| 40c7ec2 | Eddie Belter | 25 March 2016, 23:08:05 UTC | SanAndSplit: add metrics | 25 March 2016, 23:08:05 UTC |
| bf410fb | Eddie Belter | 25 March 2016, 22:01:20 UTC | SanAndSplit: streamline rg id for reads | 25 March 2016, 22:01:20 UTC |
| 0214717 | David Morton | 25 March 2016, 17:04:41 UTC | Merge pull request #1325 from davidlmorton/serviceDataFeature Use new 'service_data_to_save' feature of PTero | 25 March 2016, 17:04:41 UTC |
| 0eabc9f | Eddie Belter | 25 March 2016, 00:20:26 UTC | SanAndSplit: rework getting fh to write reads | 25 March 2016, 00:20:36 UTC |
| a198347 | Eddie Belter | 24 March 2016, 23:20:24 UTC | SanAndSplit: add tag removal to sanitize function | 24 March 2016, 23:20:24 UTC |
| aad32b7 | Eddie Belter | 24 March 2016, 23:17:13 UTC | SanAndSplit: create _sanitze_read funciton | 24 March 2016, 23:17:13 UTC |
| ed2689f | Eddie Belter | 24 March 2016, 23:05:02 UTC | SanAndSplit: merge detrermine type and get new flag functions | 24 March 2016, 23:05:35 UTC |
| 10a7023 | Eddie Belter | 24 March 2016, 22:54:39 UTC | SanAndSplit: test get new flag function | 24 March 2016, 22:54:39 UTC |
| 2dfb15d | Eddie Belter | 23 March 2016, 23:55:39 UTC | SanAndSplit: test correct seq and qual function | 24 March 2016, 22:36:15 UTC |
| f826fb3 | Eddie Belter | 23 March 2016, 23:41:22 UTC | SanAndSplit: test determine type function | 24 March 2016, 22:36:14 UTC |
| 9ea9fc4 | Eddie Belter | 22 March 2016, 20:25:14 UTC | SanSplit: add test for separate reads function | 24 March 2016, 22:36:13 UTC |
| 93f4a08 | Eddie Belter | 22 March 2016, 19:46:04 UTC | Revcomp sequence/qualities if needed | 24 March 2016, 22:36:13 UTC |
| b700148 | Eddie Belter | 22 March 2016, 19:20:19 UTC | Sanitize and Split Bam consolidate prcoess reads collect reads by template and read 1/2 remove supplementary reads only use one read 1/2 each [including non primary alignments] write all singletons to one file instead of read1/2 use set flags for read 1/2 singleton paired sanitize alignment info remove all read tags add new read group tag | 24 March 2016, 22:36:12 UTC |
| 79b271f | Eddie Belter | 11 March 2016, 23:49:36 UTC | Update WF builder | 24 March 2016, 22:36:11 UTC |
| 404ff7b | Eddie Belter | 11 March 2016, 23:20:52 UTC | Sanitize read | 24 March 2016, 22:36:10 UTC |
| 52ca1cf | Eddie Belter | 11 March 2016, 22:42:21 UTC | Sanitize headers | 24 March 2016, 22:36:09 UTC |
| d1e33cc | Eddie Belter | 11 March 2016, 22:03:37 UTC | Sanitize AND Split | 24 March 2016, 22:36:07 UTC |
| 8499ba8 | David Morton | 24 March 2016, 21:19:33 UTC | Use new 'service_data_to_save' feature of PTero This will put data from the Job services on the PTero execution's data field saving us from querying the Job service. | 24 March 2016, 21:19:33 UTC |
| a123711 | Feiyu Du | 24 March 2016, 19:11:19 UTC | add uri_unescape to import list | 24 March 2016, 19:11:19 UTC |
| 77ec114 | Feiyu Du | 24 March 2016, 16:08:49 UTC | Replace CGI with URI | 24 March 2016, 16:08:49 UTC |
| c65f33e | Feiyu Du | 24 March 2016, 16:07:42 UTC | add c_position to report | 24 March 2016, 16:07:42 UTC |
| d94a122 | Jason Walker | 23 March 2016, 14:55:50 UTC | use Text::CSV to parse CSV lines rather than simple split. | 23 March 2016, 14:55:50 UTC |
| ed2b02c | Jason Walker | 23 March 2016, 14:49:31 UTC | Merge pull request #1320 from jasonwalker80/breakdancer_novorealign_regex SV realignment compatibility with SpeedSeq BAM headers | 23 March 2016, 14:49:31 UTC |
| 3db69dd | Susanna Kiwala | 23 March 2016, 14:29:59 UTC | Merge pull request #1321 from susannasiebert/clinseq_perltidy Run all ClinSeq related commands through perltidy | 23 March 2016, 14:29:59 UTC |
| 0f75940 | Susanna Kiwala | 22 March 2016, 19:03:41 UTC | Refactor or do clauses | 23 March 2016, 14:10:21 UTC |
| 495bd38 | Susanna Kiwala | 22 March 2016, 16:21:03 UTC | perltidy GenerateClonalityPlots | 23 March 2016, 14:10:21 UTC |
| 929c004 | Susanna Kiwala | 22 March 2016, 16:19:19 UTC | perltidy Converge SummarizeSnvIndelReport | 23 March 2016, 14:10:21 UTC |
| 6c1fd93 | Susanna Kiwala | 22 March 2016, 16:18:33 UTC | perltidy Converge Stats | 23 March 2016, 14:10:20 UTC |
| 628e985 | Susanna Kiwala | 22 March 2016, 16:17:48 UTC | perltidy Converge Snvs | 23 March 2016, 14:10:20 UTC |
| 56d6297 | Susanna Kiwala | 22 March 2016, 16:17:07 UTC | perltidy Converge SnvIndelReport | 23 March 2016, 14:10:20 UTC |
| ad09465 | Susanna Kiwala | 22 March 2016, 16:16:24 UTC | perltidy Converge PlotCnvs | 23 March 2016, 14:10:20 UTC |
| 8600927 | Susanna Kiwala | 22 March 2016, 16:15:35 UTC | perltidy Converge MutationType.pm | 23 March 2016, 14:10:19 UTC |
| d81e209 | Susanna Kiwala | 22 March 2016, 16:14:48 UTC | perltidy Converge MutationSpectrum | 23 March 2016, 14:10:19 UTC |
| 7ba134b | Susanna Kiwala | 22 March 2016, 16:13:55 UTC | perltidy Converge DocmReport | 23 March 2016, 14:10:19 UTC |
| fdc1b0f | Susanna Kiwala | 22 March 2016, 16:13:04 UTC | perltidy Converge DgidbGenes | 23 March 2016, 14:10:19 UTC |
| 62e7c4d | Susanna Kiwala | 22 March 2016, 16:12:07 UTC | perltidy Converge DgidbCounts | 23 March 2016, 14:10:18 UTC |
| bd49fce | Susanna Kiwala | 22 March 2016, 16:11:17 UTC | perltidy Converge CufflinksDe | 23 March 2016, 14:10:18 UTC |
| f911950 | Susanna Kiwala | 22 March 2016, 16:09:59 UTC | perltidy Converge CancerRelevanceScore | 23 March 2016, 14:10:18 UTC |
| 45d95d9 | Susanna Kiwala | 22 March 2016, 16:07:00 UTC | perltidy Converge Base | 23 March 2016, 14:10:18 UTC |
| 6f6636f | Susanna Kiwala | 22 March 2016, 16:06:05 UTC | perltidy Converge AllEvents | 23 March 2016, 14:10:17 UTC |
| 0164fdd | Susanna Kiwala | 22 March 2016, 16:03:17 UTC | perltidy UpdateInputsFromModelGroup | 23 March 2016, 14:10:17 UTC |
| 1217f15 | Susanna Kiwala | 22 March 2016, 16:02:03 UTC | perltidy UpdateAnalysis | 23 March 2016, 14:10:17 UTC |
| c9be155 | Susanna Kiwala | 22 March 2016, 16:01:17 UTC | perltidy TophatJunctionsAbsolute | 23 March 2016, 14:10:16 UTC |
| 8be9d73 | Susanna Kiwala | 22 March 2016, 16:00:31 UTC | perltidy SummarizeTier1SnvSupport | 23 March 2016, 14:10:16 UTC |
| 3516622 | Susanna Kiwala | 22 March 2016, 15:59:37 UTC | perltidy SummarizeSvs | 23 March 2016, 14:10:16 UTC |
| 985ea57 | Susanna Kiwala | 22 March 2016, 15:59:00 UTC | perltidy SummarizeModels | 23 March 2016, 14:10:16 UTC |
| 20e8f7c | Susanna Kiwala | 22 March 2016, 15:58:09 UTC | perltidy SummarizeCnvs | 23 March 2016, 14:10:15 UTC |
| fe89fe8 | Susanna Kiwala | 22 March 2016, 15:57:24 UTC | perltidy SummarizeBuilds | 23 March 2016, 14:10:15 UTC |
| d7d68d0 | Susanna Kiwala | 22 March 2016, 15:56:42 UTC | perltidy RunCnView | 23 March 2016, 14:10:15 UTC |
| ebaa2da | Susanna Kiwala | 22 March 2016, 15:55:28 UTC | perltidy MicroarrayCnv | 23 March 2016, 14:10:15 UTC |
| 3001e49 | Susanna Kiwala | 22 March 2016, 15:53:27 UTC | perltidy MakeCircosPlot | 23 March 2016, 14:10:14 UTC |
| 2f29be9 | Susanna Kiwala | 22 March 2016, 15:46:56 UTC | perltidy ImportSnvsIndels | 23 March 2016, 14:10:14 UTC |
| 1a9e454 | Susanna Kiwala | 22 March 2016, 15:46:04 UTC | perltidy IdentifyLoh | 23 March 2016, 14:10:14 UTC |
| ae4c271 | Susanna Kiwala | 22 March 2016, 15:45:06 UTC | perltidy GetVariantSources | 23 March 2016, 14:10:14 UTC |
| a632077 | Susanna Kiwala | 22 March 2016, 15:44:15 UTC | perltidy GetBamReadCountsMatrix | 23 March 2016, 14:10:13 UTC |
| b14a349 | Susanna Kiwala | 22 March 2016, 15:43:16 UTC | perltidy GetBamReadCounts | 23 March 2016, 14:10:13 UTC |
| a5df413 | Susanna Kiwala | 22 March 2016, 15:41:58 UTC | perltidy GenerateSciclonePlots | 22 March 2016, 20:39:22 UTC |
| c5f8cca | Susanna Kiwala | 22 March 2016, 15:35:51 UTC | perltidy DumpIgvXml | 22 March 2016, 20:39:21 UTC |
| 45eafc7 | Susanna Kiwala | 22 March 2016, 15:33:00 UTC | perltidy CufflinksExpressionAbsolute | 22 March 2016, 20:26:41 UTC |
| d3244fe | Susanna Kiwala | 22 March 2016, 15:28:50 UTC | perltidy CufflinksDifferentialExpression | 22 March 2016, 20:26:41 UTC |
| 93df0c9 | Susanna Kiwala | 22 March 2016, 15:27:31 UTC | perltidy CreateWgsClonalityPlotByVariantSource | 22 March 2016, 20:26:41 UTC |
| ee0ea4d | Susanna Kiwala | 22 March 2016, 15:25:45 UTC | perltidy CreateMutationSpectrum | 22 March 2016, 20:26:40 UTC |
| d430749 | Susanna Kiwala | 22 March 2016, 15:24:22 UTC | perltidy CreateMutationSpectrum | 22 March 2016, 20:26:40 UTC |
| 5c9d401 | Susanna Kiwala | 22 March 2016, 15:21:31 UTC | perltidy AnnotateGenesByDgidb | 22 March 2016, 20:26:40 UTC |
| 053a9b6 | Susanna Kiwala | 22 March 2016, 15:20:14 UTC | perltidy AnnotateGenesByCategory | 22 March 2016, 20:26:40 UTC |
| a64eeca | Susanna Kiwala | 22 March 2016, 15:17:36 UTC | perltidy ClinSeq Util.pm | 22 March 2016, 20:26:40 UTC |
