| 80c257a | Jason Walker | 29 February 2016, 20:35:25 UTC | The necessary changes simply based on model class to get a build to start. Conflicts: lib/perl/Genome/Model/ClinSeq.pm | 25 March 2016, 17:17:54 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 |
| 2947c5e | Susanna Kiwala | 11 March 2016, 16:44:42 UTC | Refactor copy_fusion_files | 25 March 2016, 17:04:07 UTC |
| 12877bb | Susanna Kiwala | 25 March 2016, 14:44:10 UTC | Group tophat_junctions_absolute_op, cufflinks_expression_absolute_op, and intersect_tumor_fusion_sv_op together | 25 March 2016, 14:44:29 UTC |
| adedcfe | Susanna Kiwala | 25 March 2016, 14:30:59 UTC | Subroutine for annotate_genes_by_dgidb_op | 25 March 2016, 14:37:36 UTC |
| ec7f100 | Susanna Kiwala | 25 March 2016, 14:11:50 UTC | Subroutine for identify_loh_op | 25 March 2016, 14:11:50 UTC |
| f92fe61 | Susanna Kiwala | 25 March 2016, 14:09:45 UTC | Subroutine for sciclone_op | 25 March 2016, 14:09:45 UTC |
| 496c654 | Susanna Kiwala | 25 March 2016, 13:57:16 UTC | Subroutine for create_mutation_spectrum_op | 25 March 2016, 13:57:16 UTC |
| 2748799 | Susanna Kiwala | 25 March 2016, 13:48:21 UTC | Subroutine for converge_snv_indel_report_op | 25 March 2016, 13:48:21 UTC |
| c34af0c | Susanna Kiwala | 25 March 2016, 13:33:38 UTC | Subroutine for make_circos_plot_op | 25 March 2016, 13:33:38 UTC |
| 153ed45 | Susanna Kiwala | 24 March 2016, 19:47:49 UTC | Subroutine for summarize_tier1_snv_support_op | 25 March 2016, 13:29:08 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 |
| 939b02f | Susanna Kiwala | 24 March 2016, 19:11:52 UTC | Subroutine for annotate_genes_by_category_normal_rna_op | 24 March 2016, 19:24:36 UTC |
| a8ebc76 | Susanna Kiwala | 24 March 2016, 19:10:49 UTC | Subroutine for annotate_genes_by_category_tumor_rna_op | 24 March 2016, 19:24:35 UTC |
| 896e667 | Susanna Kiwala | 24 March 2016, 18:42:33 UTC | Consolidate annotate_genes_by_category_op and annotate_genes_by_category_cnv_op | 24 March 2016, 19:24:35 UTC |
| 1cf386b | Susanna Kiwala | 24 March 2016, 18:29:01 UTC | Subroutine for annotate_genes_by_category_cnv_op | 24 March 2016, 19:24:35 UTC |
| 0677cd1 | Susanna Kiwala | 24 March 2016, 18:20:31 UTC | Subroutine for annotate_genes_by_category_op | 24 March 2016, 19:24:35 UTC |
| 4655b6f | Susanna Kiwala | 24 March 2016, 17:44:45 UTC | Subroutine for summarize_svs_op | 24 March 2016, 19:21:04 UTC |
| ce44c27 | Susanna Kiwala | 24 March 2016, 17:39:12 UTC | Group clonality_op, run_cn_view_op, and summarize_cnvs_op together | 24 March 2016, 19:21:04 UTC |
| 4684771 | Susanna Kiwala | 24 March 2016, 17:37:07 UTC | Subroutine for summarize_cnvs_op | 24 March 2016, 19:21:04 UTC |
| c48f2a2 | Susanna Kiwala | 24 March 2016, 17:32:31 UTC | Subroutine for docm_report_op | 24 March 2016, 19:21:03 UTC |
| 86ac53f | Susanna Kiwala | 24 March 2016, 17:28:45 UTC | Subroutine for exome_cnv_op | 24 March 2016, 19:18:37 UTC |
| bfc849d | Susanna Kiwala | 24 March 2016, 17:18:58 UTC | Subroutine for microarray_cnv_op | 24 March 2016, 19:18:37 UTC |
| 4d16b07 | Susanna Kiwala | 24 March 2016, 17:14:33 UTC | Subroutine for run_cn_view_op | 24 March 2016, 19:18:37 UTC |
| 6f3d424 | Susanna Kiwala | 24 March 2016, 17:00:43 UTC | Subroutine for clonality_op | 24 March 2016, 19:18:36 UTC |
| 9ef9dff | Susanna Kiwala | 24 March 2016, 16:57:24 UTC | Subroutine for igv_session_op | 24 March 2016, 19:18:36 UTC |
| 56a3d08 | Susanna Kiwala | 24 March 2016, 16:26:31 UTC | Subroutine for intersect_tumor_fusion_sv_op | 24 March 2016, 19:18:36 UTC |
| 6679fac | Susanna Kiwala | 24 March 2016, 16:21:24 UTC | Subroutine for cufflinks_differential_expression_op | 24 March 2016, 19:18:36 UTC |
| 070b7fe | Susanna Kiwala | 24 March 2016, 16:12:16 UTC | Subroutine for cufflinks_expression_absolute_op | 24 March 2016, 19:18:35 UTC |
| c911fdf | Susanna Kiwala | 24 March 2016, 16:00:13 UTC | Subroutine for tophat_junctions_absolute_op | 24 March 2016, 19:18:35 UTC |
| c4b234c | Susanna Kiwala | 24 March 2016, 15:51:23 UTC | Subroutines for mutation_diagram_op and wgs_exome_build_converge_op | 24 March 2016, 19:18:35 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 |
| fa65068 | Susanna Kiwala | 24 March 2016, 15:43:20 UTC | Subroutine for variant_sources_op | 24 March 2016, 16:02:16 UTC |
| 41b3fd0 | Susanna Kiwala | 24 March 2016, 15:38:34 UTC | Subroutine for import_snvs_indels_op | 24 March 2016, 16:02:16 UTC |
| 8a1c770 | Susanna Kiwala | 24 March 2016, 15:36:06 UTC | Subroutine for summarize_builds_op | 24 March 2016, 16:02:16 UTC |
| 846ac6b | Susanna Kiwala | 23 March 2016, 20:16:12 UTC | Port ClinSeq to WorkflowBuilder | 24 March 2016, 16:02:16 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 |
| 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 |
