| 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 |
| 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 |
| 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 |
| ef92111 | Thomas B. Mooney | 16 March 2016, 21:34:49 UTC | Merge pull request #1310 from tmooney/remove_old_refcov_result Remove old RefCov result. | 16 March 2016, 21:34:49 UTC |
| 8df1ad3 | Thomas Mooney | 16 March 2016, 21:06:20 UTC | AlignAndMerge can now be run multiple times within the same dispatcher. AlignAndMerge was claiming global input names, which leads to conflicts if the instrument data do not all come from the same merge group. (The new testcase demonstrates this situation and passes with this change.) | 16 March 2016, 21:06:20 UTC |
| 53a5f78 | Thomas Mooney | 16 March 2016, 20:44:44 UTC | Fix determination of reference and instrument_data for AlignAndMerge. * The reference selection coincidentally worked by convention since we usually use the same input name in the strategy. * The instrument data happened to work because we've heretofore wanted to align *all* the data when using AlignAndMerge, but we can't assume that's true. | 16 March 2016, 20:44:44 UTC |
| 8a47b69 | Avinash Ramu | 16 March 2016, 20:20:55 UTC | Skip mutation spectrum on empty input Currently this step attempts to run mutation spectrum sequence context on an empty input which causes the downstream R module to die unpredictably. We'd like to skip running this analysis when the tier1 variant file is empty. | 16 March 2016, 20:20:55 UTC |
| 526e5cc | Ben Ainscough | 15 March 2016, 19:29:55 UTC | Merge pull request #1309 from bainscou/master added check to see existence of wgs or exome | 15 March 2016, 19:29:55 UTC |
| e762cd7 | Ben Ainscough | 15 March 2016, 19:16:30 UTC | Remove tumor_model and normal_model call | 15 March 2016, 19:16:30 UTC |
| f7fb340 | Ben Ainscough | 15 March 2016, 16:06:15 UTC | Change ordering of check to look at exome first | 15 March 2016, 16:06:15 UTC |
| 03f60b3 | Jason Walker | 15 March 2016, 15:49:29 UTC | Merge pull request #1308 from jasonwalker80/make_tiering_bed_grch38 Tiering for GRCh38 | 15 March 2016, 15:49:29 UTC |
| 3e201ae | Avi Ramu | 15 March 2016, 14:29:27 UTC | Merge pull request #1307 from gatoravi/loh_empty_files Make FilterFalsePositives not die on empty input. | 15 March 2016, 14:29:27 UTC |
| 508ec01 | Thomas Mooney | 14 March 2016, 22:41:43 UTC | Remove NO_LSF environment variable from tests not running workflows. This should have no effect on these tests. | 15 March 2016, 13:01:05 UTC |
| d7ab52c | Thomas Mooney | 14 March 2016, 20:47:49 UTC | Replace NO_LSF=1 with inline workflow_builder_backend. | 15 March 2016, 13:01:05 UTC |
| 06fec11 | Thomas Mooney | 14 March 2016, 21:06:02 UTC | Remove old RefCov result. This appears to be unused--there are no rows in the DB for this result. | 14 March 2016, 21:11:44 UTC |
| 25cc09e | Ben Ainscough | 14 March 2016, 20:05:41 UTC | added check to see existence of wgs or exome | 14 March 2016, 20:05:41 UTC |
| 3bdcbfc | Jason Walker | 14 March 2016, 16:44:57 UTC | Merge pull request #1305 from jasonwalker80/allow_empty_variants Zero size variants in CreateReport | 14 March 2016, 16:44:57 UTC |
| 8b6f1ee | Jason Walker | 14 March 2016, 15:46:59 UTC | Make an empty clean BED file. | 14 March 2016, 15:46:59 UTC |
| bd86e22 | Jason Walker | 14 March 2016, 15:02:09 UTC | organize if/else as a hash of IDs to directories. | 14 March 2016, 15:02:09 UTC |
| 36b0658 | Jason Walker | 14 March 2016, 14:56:32 UTC | Create empty files rather than skipping steps. | 14 March 2016, 14:56:32 UTC |
| 43123a5 | Thomas B. Mooney | 14 March 2016, 13:15:13 UTC | Merge pull request #1298 from tmooney/production_uses_new_prodbuilder_user Production No Longer Hardcoded to "apipe-builder". | 14 March 2016, 13:15:13 UTC |
| 8a73537 | Thomas B. Mooney | 14 March 2016, 13:13:49 UTC | Merge pull request #1295 from tmooney/get_email_from_user_object Get E-Mail Address from User Object | 14 March 2016, 13:13:49 UTC |
| d8ed15b | Thomas B. Mooney | 14 March 2016, 13:13:13 UTC | Merge pull request #1289 from tmooney/migrate_refalign_pp_to_model Migrate ReferenceAlignment Parameter Specification to the Model Class | 14 March 2016, 13:13:13 UTC |
| 6f698af | APipe Tester | 12 March 2016, 13:15:46 UTC | Updated `genome` tab completion. | 12 March 2016, 13:15:46 UTC |
| ba98a03 | Avinash Ramu | 11 March 2016, 22:55:56 UTC | Don't die on empty input. This step is run as a part of the LOH pipeline. Currently if the variant file that is passed to this module is empty, the workflow crashes with an error message(bam-readcount is invoked with an empty file which causes it to die). Instead I think we'd like this module to spit out a warning and not attempt to filter if the input is empty. | 11 March 2016, 22:55:56 UTC |
| 5ee49ca | Avinash Ramu | 11 March 2016, 21:59:05 UTC | Add ideogram for hg38 | 11 March 2016, 21:59:05 UTC |
| cfddf2f | Avinash Ramu | 11 March 2016, 21:57:48 UTC | Ignore case while checking reference base. The new reference is soft-masked, this means that regions of low complexity are in lower-case [A,C,G,T,N]. This check should pass in those regions. | 11 March 2016, 21:57:48 UTC |
| cdef72f | Avinash Ramu | 11 March 2016, 21:57:24 UTC | Remove unused variable $reference_build_ncbi_n | 11 March 2016, 21:57:24 UTC |
| d92ad82 | Avinash Ramu | 11 March 2016, 21:56:17 UTC | Skip KI contigs | 11 March 2016, 21:56:17 UTC |
| f41f4bd | Eddie Belter | 11 March 2016, 19:02:06 UTC | Merge pull request #1301 from ebelter/instdata-import-singletons InstData Import: Split by read into paireds, read1s and read2s | 11 March 2016, 19:02:06 UTC |
| 8e6e79c | Jason Walker | 11 March 2016, 16:15:28 UTC | Merge pull request #1304 from jasonwalker80/refseq_convert_by_md5 New chr_md5 reference converter | 11 March 2016, 16:15:28 UTC |
| 99153f1 | Jason Walker | 10 March 2016, 22:14:41 UTC | The original logic produced an indel file with trailing tabs instead or dbsnp rsid. Remove the test for an indels VCF since it is never produced and the original code only checked for the presence of a snvs VCF. | 10 March 2016, 22:14:41 UTC |
| 25d1b4b | Thomas B. Mooney | 10 March 2016, 22:12:47 UTC | Merge pull request #1286 from tmooney/consolidate_gmt_test_helpers Consolidate GMT TestHelpers into Genome::Utility::Test. | 10 March 2016, 22:12:47 UTC |
| 30b5fd3 | Jason Walker | 10 March 2016, 21:16:36 UTC | A few parameterized warnings and subroutine fixes. | 10 March 2016, 21:16:36 UTC |
| e14d1a0 | Jason Walker | 10 March 2016, 19:17:08 UTC | Allow for zero size variant files. | 10 March 2016, 19:17:08 UTC |
| f4e8b8c | Jason Walker | 10 March 2016, 17:03:37 UTC | Add a UCSC tiering directory for GRCh38 reference sequence build. | 10 March 2016, 17:03:37 UTC |
| 831f8ff | Jason Walker | 10 March 2016, 16:55:45 UTC | Add additional fields to more mock seqdict. | 10 March 2016, 16:55:45 UTC |
| 27c4458 | Jason Walker | 10 March 2016, 15:03:30 UTC | Add additional expected seqdict fields to mock seqdict. | 10 March 2016, 15:03:30 UTC |
