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23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
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
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
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
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
d8c4414 Susanna Kiwala 22 March 2016, 15:15:38 UTC perltidy ClinSeq.pm 22 March 2016, 20:26:40 UTC
98084e4 Avi Ramu 22 March 2016, 20:26:17 UTC Merge pull request #1318 from gatoravi/hg38-clinseq-fixes clinseq fixes for hg38 22 March 2016, 20:26:17 UTC
3f80ed3 Thomas B. Mooney 21 March 2016, 20:15:58 UTC Merge pull request #1319 from tmooney/duplication_handling_in_dispatcher_is_optional Duplication Handling in the Alignment Dispatcher Is Optional. 21 March 2016, 20:15:58 UTC
1db8213 Jason Walker 21 March 2016, 19:05:01 UTC Use whitespace to denote end of string rather than word-boundary. Non-word characters are excluded from the end of the library string such as double quotation marks. 21 March 2016, 19:05:01 UTC
225e278 Thomas Mooney 21 March 2016, 17:50:30 UTC Duplication handling is optional. 21 March 2016, 17:50:30 UTC
aff1024 Avinash Ramu 21 March 2016, 15:48:14 UTC Use fatal_message() 21 March 2016, 15:48:14 UTC
e3c687d Avinash Ramu 21 March 2016, 15:47:24 UTC Declare variable once 21 March 2016, 15:47:24 UTC
529f07e Avinash Ramu 21 March 2016, 15:46:53 UTC Avoid warning from autoloader 21 March 2016, 15:46:53 UTC
f01ba54 Avinash Ramu 21 March 2016, 15:42:26 UTC Make folder naming consistent. 21 March 2016, 15:42:26 UTC
7cd616c Avinash Ramu 21 March 2016, 15:38:14 UTC Use fatal_message() 21 March 2016, 15:38:14 UTC
3cdc454 Avinash Ramu 21 March 2016, 15:37:42 UTC Add 38 to error message 21 March 2016, 15:37:42 UTC
a2cda9d Avinash Ramu 21 March 2016, 15:36:04 UTC Remove code-remains 21 March 2016, 15:36:04 UTC
c28d308 Avinash Ramu 21 March 2016, 15:35:08 UTC Use fatal_message() 21 March 2016, 15:35:08 UTC
594cf72 Avinash Ramu 21 March 2016, 15:30:34 UTC Avoid warning from autoloader. 21 March 2016, 15:30:34 UTC
55a88e8 Thomas B. Mooney 17 March 2016, 22:57:40 UTC Merge pull request #1315 from tmooney/align_and_merge_dags_have_unique_names Support Multiple Merge Groups for AlignAndMerge in the AlignmentDispatcher 17 March 2016, 22:57:40 UTC
de8e25b Avinash Ramu 17 March 2016, 22:30:37 UTC Incorporate suggestions from #1292 17 March 2016, 22:30:37 UTC
4684f4c Avinash Ramu 17 March 2016, 22:23:17 UTC Incorporate suggestions from #1292 17 March 2016, 22:23:17 UTC
88ccc65 Thomas B. Mooney 17 March 2016, 19:29:16 UTC Merge pull request #1311 from tmooney/replace_no_lsf_with_inline_backend Replace NO_LSF with "inline" Backend 17 March 2016, 19:29:16 UTC
4e9281e Avi Ramu 17 March 2016, 17:17:57 UTC Merge pull request #1314 from gatoravi/mutation-spectrum-fix Skip mutation spectrum on empty input 17 March 2016, 17:17:57 UTC
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