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biopet.biopet
Commits
dd937c3a
Commit
dd937c3a
authored
Jul 21, 2017
by
pjvan_thof
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Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-718
parents
4989de28
9b83c7aa
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519 changed files
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6169 additions
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2767 deletions
+6169
-2767
Jenkinsfile
Jenkinsfile
+2
-2
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+1
-1
bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
...sc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
+1
-1
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
...lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
+2
-2
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+2
-2
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+1
-1
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+5
-7
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+1
-1
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
+7
-7
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
...c/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
+3
-4
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
...c/biopet/core/report/ext/css/sortable-theme-bootstrap.css
+1
-3
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/files.ssp
.../main/resources/nl/lumc/sasc/biopet/core/report/files.ssp
+3
-3
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
...c/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
+4
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+10
-10
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
+4
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+6
-6
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
+6
-5
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+24
-19
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PedigreeQscript.scala
...main/scala/nl/lumc/sasc/biopet/core/PedigreeQscript.scala
+224
-0
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+4
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+6
-5
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
...rc/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
.../scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
+3
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala
...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala
+2
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+19
-8
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
...a/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
...in/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
+6
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/pipelinestatus/Deps.scala
.../scala/nl/lumc/sasc/biopet/core/pipelinestatus/Deps.scala
+108
-0
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/pipelinestatus/Job.scala
...n/scala/nl/lumc/sasc/biopet/core/pipelinestatus/Job.scala
+66
-0
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/pipelinestatus/PipelineStatus.scala
...lumc/sasc/biopet/core/pipelinestatus/PipelineStatus.scala
+142
-111
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+4
-6
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+9
-10
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+8
-8
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
...scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
+3
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
...la/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
+15
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
...umc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
+3
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
.../nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
...sc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
...nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/CheckValidateAnnotation.scala
...asc/biopet/extensions/tools/CheckValidateAnnotation.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
...c/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
+2
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
.../nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
+8
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala
+1
-6
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
...umc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
...a/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
+5
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala
...a/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala
+2
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
...la/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
+4
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/NcbiReportToContigMap.scala
.../sasc/biopet/extensions/tools/NcbiReportToContigMap.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
...la/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/RefflatStats.scala
...a/nl/lumc/sasc/biopet/extensions/tools/RefflatStats.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
...nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
...lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
+3
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
...mc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
.../scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
+3
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
...a/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
+2
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
+2
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateAnnotation.scala
...umc/sasc/biopet/extensions/tools/ValidateAnnotation.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala
.../nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateVcf.scala
...la/nl/lumc/sasc/biopet/extensions/tools/ValidateVcf.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
...scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
+3
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala
.../nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
...ala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
.../nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
+5
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
+11
-11
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
+1
-1
biopet-core/src/test/resources/full.ped
biopet-core/src/test/resources/full.ped
+6
-0
biopet-core/src/test/resources/trio.ped
biopet-core/src/test/resources/trio.ped
+3
-0
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
.../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
+4
-4
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
...a/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
...ala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
+15
-7
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PedigreeQScriptTest.scala
.../scala/nl/lumc/sasc/biopet/core/PedigreeQScriptTest.scala
+270
-0
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
.../scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
+2
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biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
...t/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
+2
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
...c/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
+6
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biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
...scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
+2
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
...test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
+2
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
...cala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
+10
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biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
.../nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
+9
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biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala
...asc/biopet/core/report/MultisampleReportBuilderTest.scala
+0
-3
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
...a/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
+4
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biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala
...a/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
...a/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
+3
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biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
...nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
+7
-7
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
+5
-5
biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala
.../nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala
+23
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biopet-extensions/pom.xml
biopet-extensions/pom.xml
+0
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cp.scala
...ns/src/main/scala/nl/lumc/sasc/biopet/extensions/Cp.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+7
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+4
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+7
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
.../scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+6
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+9
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+2
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+11
-8
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+10
-9
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+8
-6
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+9
-7
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
+7
-5
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+7
-5
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+5
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
.../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsReheader.scala
...mc/sasc/biopet/extensions/bcftools/BcftoolsReheader.scala
+47
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
+6
-6
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+4
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
.../lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
+11
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
...l/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
+3
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
.../scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
+8
-6
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
...scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
+7
-5
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
.../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
...a/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
...l/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
+2
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
...sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
+15
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCallerCall.scala
...l/lumc/sasc/biopet/extensions/delly/DellyCallerCall.scala
+75
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
...in/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
+87
-62
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCAssessSignificancePlot.scala
...biopet/extensions/freec/FreeCAssessSignificancePlot.scala
+3
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
...a/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
...a/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
+3
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
.../lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
+11
-10
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
+17
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
+31
-30
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
+10
-10
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
...la/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
+15
-13
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+23
-21
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala
...nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala
+83
-81
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ContEst.scala
...n/scala/nl/lumc/sasc/biopet/extensions/gatk/ContEst.scala
+75
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
...nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala
...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala
+16
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
...a/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
+23
-21
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+89
-87
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
.../nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
+29
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/MuTect2.scala
...n/scala/nl/lumc/sasc/biopet/extensions/gatk/MuTect2.scala
+214
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
...cala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
+15
-13
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
.../sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
+12
-11
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
.../nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
+47
-45
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+54
-52
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
...l/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
+22
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
...ala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
+27
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
...umc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
+35
-34
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/BqsrGather.scala
.../lumc/sasc/biopet/extensions/gatk/gather/BqsrGather.scala
+3
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/CatVariantsGatherer.scala
...c/biopet/extensions/gatk/gather/CatVariantsGatherer.scala
+6
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/GatherBamFiles.scala
...c/sasc/biopet/extensions/gatk/gather/GatherBamFiles.scala
+29
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/GatherVcfs.scala
.../lumc/sasc/biopet/extensions/gatk/gather/GatherVcfs.scala
+29
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/MergeSamFiles.scala
...mc/sasc/biopet/extensions/gatk/gather/MergeSamFiles.scala
+6
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/scatter/ContigScatterFunction.scala
...iopet/extensions/gatk/scatter/ContigScatterFunction.scala
+3
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/scatter/GATKScatterFunction.scala
.../biopet/extensions/gatk/scatter/GATKScatterFunction.scala
+12
-10
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/scatter/LocusScatterFunction.scala
...biopet/extensions/gatk/scatter/LocusScatterFunction.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
...scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
+8
-6
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
+7
-5
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala
...n/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala
+8
-6
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
...la/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
+4
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
...in/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
...sc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
...c/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
...c/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
...c/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala
...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
...umc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
.../sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
.../sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala
+3
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
...nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
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-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectHsMetrics.scala
...lumc/sasc/biopet/extensions/picard/CollectHsMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+5
-5
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
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-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
.../biopet/extensions/picard/CollectTargetedPcrMetrics.scala
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-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
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-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CreateSequenceDictionary.scala
...c/biopet/extensions/picard/CreateSequenceDictionary.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
...l/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherVcfs.scala
...la/nl/lumc/sasc/biopet/extensions/picard/GatherVcfs.scala
+50
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/NormalizeFasta.scala
...l/lumc/sasc/biopet/extensions/picard/NormalizeFasta.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+12
-11
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+4
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+12
-12
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
...ala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
+9
-7
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
...nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
...a/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
...nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
.../sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
...scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
...ala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
+7
-5
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
...mc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
...la/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
...mc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
.../nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
.../lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
+4
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
+3
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
...in/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala
...la/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stouffbed/Stouffbed.scala
.../nl/lumc/sasc/biopet/extensions/stouffbed/Stouffbed.scala
+22
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stouffbed/StouffbedHorizontal.scala
...asc/biopet/extensions/stouffbed/StouffbedHorizontal.scala
+23
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stouffbed/StouffbedVertical.scala
.../sasc/biopet/extensions/stouffbed/StouffbedVertical.scala
+26
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/taxextract/TaxExtract.scala
...l/lumc/sasc/biopet/extensions/taxextract/TaxExtract.scala
+4
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/taxextract/TaxExtractCount.scala
...c/sasc/biopet/extensions/taxextract/TaxExtractCount.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/taxextract/TaxExtractExtract.scala
...sasc/biopet/extensions/taxextract/TaxExtractExtract.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
...a/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
...cala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
...c/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
+6
-10
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
...scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
+5
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
...scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
+6
-4
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/Wisecondor.scala
...l/lumc/sasc/biopet/extensions/wisecondor/Wisecondor.scala
+38
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorCount.scala
...c/sasc/biopet/extensions/wisecondor/WisecondorCount.scala
+23
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala
...sc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala
+32
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorNewRef.scala
.../sasc/biopet/extensions/wisecondor/WisecondorNewRef.scala
+28
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorZscore.scala
.../sasc/biopet/extensions/wisecondor/WisecondorZscore.scala
+27
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
...main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
+4
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
...cala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
...umc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
...a/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
...n/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
+1
-1
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala
...t/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala
+1
-1
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
...t/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
+3
-3
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala
...est/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala
+1
-1
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+4
-4
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
...scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
+4
-4
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
...test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
+15
-15
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala
...c/sasc/biopet/extensions/VariantEffectPredictorTest.scala
+3
-4
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/XhmmTest.scala
.../test/scala/nl/lumc/sasc/biopet/extensions/XhmmTest.scala
+1
-1
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
...lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
+12
-23
biopet-package/pom.xml
biopet-package/pom.xml
+10
-0
biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala
...main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala
+2
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
+76
-30
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+4
-4
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
+1
-23
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
...cala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
+14
-14
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+2
-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractTagsFromGtf.scala
.../scala/nl/lumc/sasc/biopet/tools/ExtractTagsFromGtf.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala
+2
-3
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
...in/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
+4
-5
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
+3
-5
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GtfToRefflat.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/GtfToRefflat.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
.../scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
+4
-3
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+5
-6
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+3
-3
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MultiCoverage.scala
.../main/scala/nl/lumc/sasc/biopet/tools/MultiCoverage.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/NcbiReportToContigMap.scala
...ala/nl/lumc/sasc/biopet/tools/NcbiReportToContigMap.scala
+0
-4
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
.../main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
+2
-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+2
-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToConfig.scala
.../scala/nl/lumc/sasc/biopet/tools/SamplesTsvToConfig.scala
+1
-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
...ls/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
+3
-4
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
+4
-6
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateAnnotation.scala
.../scala/nl/lumc/sasc/biopet/tools/ValidateAnnotation.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
.../main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
+6
-5
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateVcf.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/ValidateVcf.scala
+4
-4
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+5
-5
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
...s/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
+4
-4
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+1
-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+6
-6
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+2
-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
...n/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
+2
-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
.../scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
+3
-3
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
...main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
+2
-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala
...a/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
...l/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
+11
-11
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/refflatstats/RegionStats.scala
.../nl/lumc/sasc/biopet/tools/refflatstats/RegionStats.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
...main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala
...la/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala
+6
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssemblyTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatchTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/NcbiReportToContigMapTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ReplaceContigsGtfFileTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToConfigTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
...t/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala
.../scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstatTest.scala
.../lumc/sasc/biopet/tools/flagstat/BiopetFlagstatTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/refflatstats/RefflatStatsTest.scala
...umc/sasc/biopet/tools/refflatstats/RefflatStatsTest.scala
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biopet-utils/pom.xml
biopet-utils/pom.xml
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biopet-utils/src/main/resources/application.conf
biopet-utils/src/main/resources/application.conf
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/FastaUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/LazyCheck.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
...ls/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/MainCommand.scala
...rc/main/scala/nl/lumc/sasc/biopet/utils/MainCommand.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala
...s/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/SemanticVersion.scala
...ain/scala/nl/lumc/sasc/biopet/utils/SemanticVersion.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ToolCommand.scala
...rc/main/scala/nl/lumc/sasc/biopet/utils/ToolCommand.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
...s/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/annotation/Feature.scala
.../scala/nl/lumc/sasc/biopet/utils/annotation/Feature.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
.../main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala
.../scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueIndex.scala
...a/nl/lumc/sasc/biopet/utils/config/ConfigValueIndex.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala
.../scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
...a/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
...ls/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/pim/Pim.scala
...ls/src/main/scala/nl/lumc/sasc/biopet/utils/pim/Pim.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/process/AsyncProcess.scala
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-4
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
...ain/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/ScatterPlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/BamUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/IoUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValueTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
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.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
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carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
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docs/pipelines/mapping.md
docs/pipelines/mapping.md
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docs/pipelines/multisample/shiva.md
docs/pipelines/multisample/shiva.md
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flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
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flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
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flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
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flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
.../sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CheckValidateFastq.scala
.../sasc/biopet/pipelines/flexiprep/CheckValidateFastq.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
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gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
.../nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/ExtractUnmappedReads.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
...l/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
.../lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/BiomToKronaTest.scala
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/KrakenToKronaTest.scala
.../lumc/sasc/biopet/pipelines/gears/KrakenToKronaTest.scala
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generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomes.scala
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generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/FastaMerging.scala
.../sasc/biopet/pipelines/generateindexes/FastaMerging.scala
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generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfig.scala
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generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
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generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/RenderReadmeTest.scala
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generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfigTest.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
...sc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
...c/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
...pet/pipelines/gentrap/measures/CufflinksMeasurement.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala
...c/biopet/pipelines/gentrap/measures/CufflinksStrict.scala
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-2
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
.../biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
+3
-2
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
...c/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
+2
-2
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
...lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
+4
-4
gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+15
-14
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
+1
-1
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
...mc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
+0
-22
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala
.../sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala
+4
-4
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Spec.scala
.../nl/lumc/sasc/biopet/pipelines/gwastest/impute/Spec.scala
+1
-3
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
...nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
+5
-5
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
...asc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
+7
-7
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
+7
-6
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
...c/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
+3
-3
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala
...lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala
+2
-2
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
.../sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
+5
-4
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
...mc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
+2
-2
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
...umc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
+0
-8
kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
+7
-7
mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
...es/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
+2
-2
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+2
-1
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
...mc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+1
-2
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
.../biopet/pipelines/mapping/scripts/TophatRecondition.scala
+2
-2
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/template/MultiSampleMapping.scala
...iopet/pipelines/mapping/template/MultiSampleMapping.scala
+2
-2
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+9
-9
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
...asc/biopet/pipelines/mapping/MultisampleMappingTest.scala
+20
-24
pom.xml
pom.xml
+1
-0
sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+6
-12
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
+8
-11
shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariantsSv.ssp
.../nl/lumc/sasc/biopet/pipelines/shiva/sampleVariantsSv.ssp
+2
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/GenotypeGvcfs.scala
...a/nl/lumc/sasc/biopet/pipelines/shiva/GenotypeGvcfs.scala
+2
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+21
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+3
-4
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingReport.scala
...mc/sasc/biopet/pipelines/shiva/ShivaSvCallingReport.scala
+10
-13
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+54
-12
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
...c/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+2
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
+39
-25
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+4
-4
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
...sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
...pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
...asc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCaller.scala
...opet/pipelines/shiva/variantcallers/HaplotypeCaller.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
...ipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
...c/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyper.scala
...pet/pipelines/shiva/variantcallers/UnifiedGenotyper.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
...pelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
...pelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/somatic/MuTect2.scala
...opet/pipelines/shiva/variantcallers/somatic/MuTect2.scala
+98
-0
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/somatic/SomaticVariantCaller.scala
...s/shiva/variantcallers/somatic/SomaticVariantCaller.scala
+11
-0
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
...lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+26
-16
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+26
-26
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+66
-22
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
...elines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
+1
-1
tarmac/pom.xml
tarmac/pom.xml
+51
-0
tarmac/src/main/resources/nl/lumc/sasc/biopet/pipelines/tarmac/scripts/bed_threshold.py
...umc/sasc/biopet/pipelines/tarmac/scripts/bed_threshold.py
+78
-0
tarmac/src/main/resources/nl/lumc/sasc/biopet/pipelines/tarmac/scripts/find_all_common.py
...c/sasc/biopet/pipelines/tarmac/scripts/find_all_common.py
+41
-0
tarmac/src/main/resources/nl/lumc/sasc/biopet/pipelines/tarmac/scripts/select_sample_from_matrix.py
...pet/pipelines/tarmac/scripts/select_sample_from_matrix.py
+55
-0
tarmac/src/main/resources/nl/lumc/sasc/biopet/pipelines/tarmac/scripts/tarmac_plot.py
.../lumc/sasc/biopet/pipelines/tarmac/scripts/tarmac_plot.py
+99
-0
tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/Tarmac.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/tarmac/Tarmac.scala
+656
-0
tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/scripts/BedThreshold.scala
...c/sasc/biopet/pipelines/tarmac/scripts/BedThreshold.scala
+30
-0
tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/scripts/FindAllCommon.scala
.../sasc/biopet/pipelines/tarmac/scripts/FindAllCommon.scala
+31
-0
tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/scripts/SampleFromMatrix.scala
...sc/biopet/pipelines/tarmac/scripts/SampleFromMatrix.scala
+30
-0
tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/scripts/TarmacPlot.scala
...umc/sasc/biopet/pipelines/tarmac/scripts/TarmacPlot.scala
+42
-0
tarmac/src/test/resources/trio.ped
tarmac/src/test/resources/trio.ped
+3
-0
tarmac/src/test/scala/nl/lumc/sasc/biopet/pipelines/tarmac/TarmacTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/tarmac/TarmacTest.scala
+259
-0
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
...scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
+6
-5
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
+7
-7
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterImport.scala
...sc/biopet/pipelines/toucan/ManweActivateAfterImport.scala
+5
-5
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
.../biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
+5
-5
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+2
-2
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
+2
-2
No files found.
Jenkinsfile
View file @
dd937c3a
...
...
@@ -29,7 +29,7 @@ node('local') {
sh
'mkdocs build --clean --strict'
}
if
(
currentBuild
.
result
==
null
||
"SUCCESS"
.
equals
(
currentBuild
.
result
)
)
{
if
(
currentBuild
.
result
==
null
||
"SUCCESS"
==
currentBuild
.
result
)
{
currentBuild
.
result
=
"SUCCESS"
slackSend
(
color:
'#00FF00'
,
message:
"${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)"
,
channel:
'#biopet-bot'
,
teamDomain:
'lumc'
,
tokenCredentialId:
'lumc'
)
}
else
{
...
...
@@ -37,7 +37,7 @@ node('local') {
}
}
catch
(
e
)
{
if
(
currentBuild
.
result
==
null
||
"FAILED"
.
equals
(
currentBuild
.
result
)
)
{
if
(
currentBuild
.
result
==
null
||
"FAILED"
==
currentBuild
.
result
)
{
currentBuild
.
result
=
"FAILED"
}
slackSend
(
color:
'#FF0000'
,
message:
"${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)"
,
channel:
'#biopet-bot'
,
teamDomain:
'lumc'
,
tokenCredentialId:
'lumc'
)
...
...
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
dd937c3a
...
...
@@ -31,7 +31,7 @@ class Bam2Wig(val parent: Configurable) extends QScript with BiopetQScript {
def
this
()
=
this
(
null
)
@Input
(
doc
=
"Input bam file"
,
required
=
true
)
var
bamFile
:
File
=
null
var
bamFile
:
File
=
_
def
init
()
:
Unit
=
{
inputFiles
:+=
new
InputFile
(
bamFile
)
...
...
bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
View file @
dd937c3a
...
...
@@ -32,7 +32,7 @@ class BamToChromSizesTest extends TestNGSuite with Matchers {
}
@Test
def
testChromSizes
:
Unit
=
{
def
testChromSizes
()
:
Unit
=
{
val
bamFile
=
new
File
(
resourcePath
(
"/empty.bam"
))
val
bamToChromSizes
=
new
BamToChromSizes
(
null
)
bamToChromSizes
.
bamFile
=
bamFile
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
View file @
dd937c3a
...
...
@@ -13,8 +13,8 @@
<tr><th>Version</th><td>${run.version}</td></tr>
<tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
<tr><th>Output directory</th><td>${run.outputDir}</td></tr>
<tr><th>Sample</th><td>${allSamples.fi
lter(_.id == sampleId.get).headOption
.map(_.name)}</td></tr>
<tr><th>Library</th><td>${allLibraries.fi
lter(_.id == libId.get).headOption
.map(_.name)}</td></tr>
<tr><th>Sample</th><td>${allSamples.fi
nd(_.id == sampleId.get)
.map(_.name)}</td></tr>
<tr><th>Library</th><td>${allLibraries.fi
nd(_.id == libId.get)
.map(_.name)}</td></tr>
</tbody>
</table>
<br/>
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
dd937c3a
...
...
@@ -48,7 +48,7 @@ class BamMetrics(val parent: Configurable)
override
def
defaults
=
Map
(
"bedtoolscoverage"
->
Map
(
"sorted"
->
true
))
/** returns files to store in summary */
def
summaryFiles
=
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"reference"
->
referenceFasta
(),
"input_bam"
->
inputBam
)
++
ampliconBedFile
.
map
(
"amplicon"
->
_
).
toMap
++
ampliconBedFile
.
map
(
x
=>
"roi_"
+
x
.
getName
.
stripSuffix
(
".bed"
)
->
x
).
toMap
...
...
@@ -58,7 +58,7 @@ class BamMetrics(val parent: Configurable)
Map
(
"amplicon_name"
->
ampliconBedFile
.
collect
{
case
x
=>
x
.
getName
.
stripSuffix
(
".bed"
)
},
"roi_name"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)))
override
def
reportClass
=
{
override
def
reportClass
:
Some
[
BammetricsReport
]
=
{
val
bammetricsReport
=
new
BammetricsReport
(
this
)
bammetricsReport
.
outputDir
=
new
File
(
outputDir
,
"report"
)
bammetricsReport
.
summaryDbFile
=
summaryDbFile
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
dd937c3a
...
...
@@ -487,7 +487,7 @@ object BammetricsReport extends ReportBuilder {
}
def
writeTableToTsv
(
tsvFile
:
File
,
table
:
Map
[
String
,
Array
[
Any
]],
firstColumn
:
String
)
:
Unit
=
{
require
(
table
.
map
(
_
.
_2
.
size
).
toList
.
distinct
.
size
==
1
,
require
(
table
.
map
(
_
.
_2
.
length
).
toList
.
distinct
.
size
==
1
,
"Not all values has the same number or rows"
)
val
keys
=
table
.
keys
.
filterNot
(
_
==
firstColumn
).
toList
.
sorted
val
writer
=
new
PrintWriter
(
tsvFile
)
...
...
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
dd937c3a
...
...
@@ -44,7 +44,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
}
@DataProvider
(
name
=
"bammetricsOptions"
)
def
bammetricsOptions
=
{
def
bammetricsOptions
:
Array
[
Array
[
AnyVal
]]
=
{
val
rois
=
Array
(
0
,
1
,
2
,
3
)
val
bool
=
Array
(
true
,
false
)
...
...
@@ -57,7 +57,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
private
var
dirs
:
List
[
File
]
=
Nil
@Test
(
dataProvider
=
"bammetricsOptions"
)
def
testBamMetrics
(
rois
:
Int
,
amplicon
:
Boolean
,
rna
:
Boolean
,
wgs
:
Boolean
)
=
{
def
testBamMetrics
(
rois
:
Int
,
amplicon
:
Boolean
,
rna
:
Boolean
,
wgs
:
Boolean
)
:
Unit
=
{
val
outputDir
=
Files
.
createTempDir
()
dirs
:+=
outputDir
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
outputDir
,
...
...
@@ -74,8 +74,6 @@ class BamMetricsTest extends TestNGSuite with Matchers {
bammetrics
.
libId
=
Some
(
"1"
)
bammetrics
.
script
()
var
regions
:
Int
=
rois
+
(
if
(
amplicon
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectRnaSeqMetrics
])
shouldBe
(
if
(
rna
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectWgsMetrics
])
shouldBe
(
if
(
wgs
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectMultipleMetrics
])
shouldBe
1
...
...
@@ -86,13 +84,13 @@ class BamMetricsTest extends TestNGSuite with Matchers {
}
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
@AfterClass
def
removeTempOutputDir
()
:
Unit
=
{
dirs
.
foreach
(
FileUtils
.
deleteDirectory
)
}
}
object
BamMetricsTest
{
val
inputDir
=
Files
.
createTempDir
()
val
inputDir
:
File
=
Files
.
createTempDir
()
val
bam
=
new
File
(
inputDir
,
"bla.bam"
)
Files
.
touch
(
bam
)
...
...
@@ -100,7 +98,7 @@ object BamMetricsTest {
Files
.
touch
(
ampliconBed
)
def
roi
(
i
:
Int
)
:
File
=
{
val
roi
=
new
File
(
inputDir
,
s
"roi$
{i}
.bed"
)
val
roi
=
new
File
(
inputDir
,
s
"roi$
i
.bed"
)
Files
.
touch
(
roi
)
roi
}
...
...
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
dd937c3a
...
...
@@ -42,7 +42,7 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
def
variantcallers
=
List
(
"unifiedgenotyper"
)
val
numBoot
=
config
(
"boot_runs"
,
default
=
100
,
namespace
=
"raxml"
).
asInt
val
numBoot
:
Int
=
config
(
"boot_runs"
,
default
=
100
,
namespace
=
"raxml"
).
asInt
override
def
defaults
=
Map
(
"ploidy"
->
1
,
...
...
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
dd937c3a
...
...
@@ -48,7 +48,7 @@ class BastyTest extends TestNGSuite with Matchers {
}
@DataProvider
(
name
=
"bastyOptions"
)
def
bastyOptions
=
{
def
bastyOptions
:
Array
[
Array
[
Any
]]
=
{
for
(
s1
<-
sample1
;
s2
<-
sample2
)
yield
Array
(
""
,
s1
,
s2
)
}
...
...
@@ -114,7 +114,7 @@ class BastyTest extends TestNGSuite with Matchers {
numberSamples
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BaseRecalibrator
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
(
numberLibs
*
2
)
numberLibs
*
2
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
PrintReads
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
numberLibs
...
...
@@ -125,7 +125,7 @@ class BastyTest extends TestNGSuite with Matchers {
pipeline
.
summaryFiles
shouldBe
Map
()
pipeline
.
samples
foreach
{
case
(
sampleId
,
sample
)
=>
case
(
_
,
sample
)
=>
sample
.
summarySettings
shouldBe
Map
()
sample
.
summaryFiles
.
get
(
"variants_fasta"
)
should
not
be
None
sample
.
summaryFiles
.
get
(
"consensus_fasta"
)
should
not
be
None
...
...
@@ -135,7 +135,7 @@ class BastyTest extends TestNGSuite with Matchers {
sample
.
summaryFiles
.
get
(
"snps_only_consensus_variants_fasta"
)
should
not
be
None
sample
.
summaryStats
shouldBe
Map
()
sample
.
libraries
.
foreach
{
case
(
libId
,
lib
)
=>
case
(
_
,
lib
)
=>
lib
.
summarySettings
shouldBe
Map
()
lib
.
summaryFiles
shouldBe
Map
()
lib
.
summaryStats
shouldBe
Map
()
...
...
@@ -154,14 +154,14 @@ class BastyTest extends TestNGSuite with Matchers {
}
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
@AfterClass
def
removeTempOutputDir
()
:
Unit
=
{
dirs
.
foreach
(
FileUtils
.
deleteDirectory
)
}
}
object
BastyTest
{
def
outputDir
=
Files
.
createTempDir
()
val
inputDir
=
Files
.
createTempDir
()
def
outputDir
:
File
=
Files
.
createTempDir
()
val
inputDir
:
File
=
Files
.
createTempDir
()
def
inputTouch
(
name
:
String
)
:
String
=
{
val
file
=
new
File
(
inputDir
,
name
)
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
View file @
dd937c3a
...
...
@@ -150,10 +150,9 @@ body {
float
:
right
;
width
:
0
;
height
:
0
;
border-color
:
transparent
;
border-style
:
solid
;
border-width
:
5px
0
5px
5px
;
border-left-color
:
#cccccc
;
border
:
5px
solid
transparent
;
border-right-width
:
0
;
border-left-color
:
#cccccc
;
margin-top
:
5px
;
margin-right
:
-10px
;
}
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
View file @
dd937c3a
...
...
@@ -46,9 +46,7 @@ table[data-sortable] th:after {
vertical-align
:
inherit
;
height
:
0
;
width
:
0
;
border-width
:
5px
;
border-style
:
solid
;
border-color
:
transparent
;
border
:
5px
solid
transparent
;
margin-right
:
1px
;
margin-left
:
10px
;
float
:
right
;
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/files.ssp
View file @
dd937c3a
...
...
@@ -31,9 +31,9 @@
<tbody>
#for (file <- files)
<tr><td>${allPipelines.find(_.id == file.pipelineId).map(_.name)}</td>
<td>${file.moduleId.
map(id => allModules.find(x => x.pipelineId == file.pipelineId && file.moduleId == id).map(_.name)).flatten.getOrElse(("-")
)}</td>
<td>${file.sampleId.
map(id => allSamples.find(_.id == id).map(_.name)).flatten.getOrElse(("-")
)}</td>
<td>${file.libraryId.
map(id => allLibraries.find(_.id == id).map(_.name)).flatten.getOrElse(("-")
)}</td>
<td>${file.moduleId.
flatMap(id => allModules.find(x => x.pipelineId == file.pipelineId && file.moduleId == id).map(_.name)).getOrElse("-"
)}</td>
<td>${file.sampleId.
flatMap(id => allSamples.find(_.id == id).map(_.name)).getOrElse("-"
)}</td>
<td>${file.libraryId.
flatMap(id => allLibraries.find(_.id == id).map(_.name)).getOrElse("-"
)}</td>
<td>${file.key}</td>
<td>${file.path}</td>
<td>${file.md5}</td></tr>
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
View file @
dd937c3a
...
...
@@ -42,7 +42,7 @@
val tabIndex = if (first) " tabindex='-1'" else ""
// val listGroupA = if(subPage._2.subPages.nonEmpty) "list-group-item" else ""
va
r
menuItem: String = "
<li
class=
'%s'
>
".format(listSubmenu) +
va
l
menuItem: String = "
<li
class=
'%s'
>
".format(listSubmenu) +
"
<a
href=
'%s'
class=
'%s'
%
s
>
".format(href, "", tabIndex) +
"%s".format(subPageName) +
"
</a>
" +
...
...
@@ -93,7 +93,7 @@
<script
language=
"JavaScript"
>
<!--
$
(
document
).
ready
(
function
()
{
Sortable
.
init
()
Sortable
.
init
()
;
$
(
'
body
'
).
scrollspy
({
target
:
'
.bs-sidebar
'
...
...
@@ -135,14 +135,14 @@
<a
href=
"${rootPath}index.html"
>
Home
#if (iPage.subPages.nonEmpty)
<b
class=
"caret"
></b>
#end
</a>
${unescape(createMenu(iPage, Nil, false))}
${unescape(createMenu(iPage, Nil, f
irst = f
alse))}
</li>
#else
<li
class=
"root #if (t == path.size) active #end"
>
<a
href=
"${rootPath}${path.slice(0,t).mkString("
",
"/",
"/")}
index.html
"
>
${path( t - 1 )}
#if (getSubPage(path.slice(0, t)).subPages.nonEmpty)
<b
class=
"caret"
></b>
#end
</a>
${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t), false))}
${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t), f
irst = f
alse))}
</li>
#end
#end
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
dd937c3a
...
...
@@ -60,10 +60,10 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
}
/**
*
This value is used to let you job wait a x number of second after it finish.
*
This is ionly used when having storage delay issues
* This value is used to let you job wait a x number of second after it finish.
* This is ionly used when having storage delay issues
*/
va
r
jobDelayTime
:
Option
[
Int
]
=
config
(
"job_delay_time"
)
va
l
jobDelayTime
:
Option
[
Int
]
=
config
(
"job_delay_time"
)
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun
=
{
...
...
@@ -147,9 +147,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
}
private
[
core
]
var
_inputAsStdin
=
false
def
inputAsStdin
=
_inputAsStdin
def
inputAsStdin
:
Boolean
=
_inputAsStdin
private
[
core
]
var
_outputAsStdout
=
false
def
outputAsStdout
=
_outputAsStdout
def
outputAsStdout
:
Boolean
=
_outputAsStdout
/**
* This operator sends stdout to `that` and combine this into 1 command line function
...
...
@@ -212,13 +212,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
maxGroups
:
Int
=
0
)
:
String
=
{
if
(
values
.
size
%
groupSize
!=
0
)
Logging
.
addError
(
s
"Arg '$
{argName}' values: '${values}' does not fit to a groupSize of ${groupSize}
"
)
s
"Arg '$
argName' values: '$values' does not fit to a groupSize of $groupSize
"
)
val
groups
=
values
.
size
/
groupSize
if
(
groups
<
minGroups
)
Logging
.
addError
(
s
"Args '$
{argName}
' need atleast $minGroups with size $groupSize"
)
Logging
.
addError
(
s
"Args '$
argName
' need atleast $minGroups with size $groupSize"
)
if
(
maxGroups
>
0
&&
groups
>
maxGroups
)
Logging
.
addError
(
s
"Args '$
{argName}
' may only have $maxGroups with size $groupSize"
)
if
(
values
.
nonEmpty
)
required
(
argName
)
+
values
.
map
(
required
(
_
)
).
mkString
Logging
.
addError
(
s
"Args '$
argName
' may only have $maxGroups with size $groupSize"
)
if
(
values
.
nonEmpty
)
required
(
argName
)
+
values
.
map
(
required
).
mkString
else
""
}
...
...
@@ -251,7 +251,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
}
private
[
core
]
var
_pipesJobs
:
List
[
BiopetCommandLineFunction
]
=
Nil
def
pipesJobs
=
_pipesJobs
def
pipesJobs
:
List
[
BiopetCommandLineFunction
]
=
_pipesJobs
def
addPipeJob
(
job
:
BiopetCommandLineFunction
)
{
_pipesJobs
:+=
job
_pipesJobs
=
_pipesJobs
.
distinct
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
dd937c3a
...
...
@@ -30,7 +30,7 @@ trait BiopetJavaCommandLineFunction
override
def
defaultVmemFactor
:
Double
=
2.0
/** Constructs java opts, this adds scala threads */
override
def
javaOpts
=
override
def
javaOpts
:
String
=
super
.
javaOpts
+
optional
(
"-Dscala.concurrent.context.numThreads="
,
threads
,
spaceSeparated
=
false
)
+
optional
(
"-Dscala.concurrent.context.maxThreads="
,
threads
,
spaceSeparated
=
false
)
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
View file @
dd937c3a
...
...
@@ -30,14 +30,14 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
lazy
val
input
:
List
[
File
]
=
try
{