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biopet.biopet
Commits
e5bbde4d
Commit
e5bbde4d
authored
Apr 26, 2017
by
Ruben Vorderman
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Formatted scala files with scalafmt
parent
1e95dc46
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497 changed files
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20707 additions
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16002 deletions
+20707
-16002
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+19
-19
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+19
-19
bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
...sc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
+17
-16
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+77
-54
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+262
-123
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
...lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
+16
-15
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
+21
-20
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+29
-28
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+78
-44
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
+78
-63
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+82
-70
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
+22
-23
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+21
-18
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
+28
-23
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+64
-43
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
+44
-30
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+90
-56
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+47
-32
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
.../main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
+138
-58
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+98
-66
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
...ain/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
+19
-19
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala
.../nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala
+18
-17
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
...rc/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
+73
-43
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
.../scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
+15
-15
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala
...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala
+30
-25
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+75
-51
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
...la/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
+38
-23
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
...a/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
+19
-19
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
...in/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
+16
-15
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
...sc/biopet/core/extensions/PythonCommandLineFunction.scala
+21
-21
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
...c/biopet/core/extensions/RscriptCommandLineFunction.scala
+17
-17
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
...mc/sasc/biopet/core/report/MultisampleReportBuilder.scala
+37
-27
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+132
-88
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
...in/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
+19
-19
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
+24
-24
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
...scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
+23
-23
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+66
-52
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+240
-80
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+99
-79
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
.../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
+23
-21
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
...a/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
+21
-18
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
...ala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
+74
-63
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
.../scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
+15
-15
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
...t/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
+20
-18
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
...c/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
+45
-37
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
...scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
+16
-16
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
...test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
+16
-18
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
...cala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
+25
-19
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
.../nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
+47
-33
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala
...asc/biopet/core/report/MultisampleReportBuilderTest.scala
+28
-21
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
...a/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
+28
-22
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala
...a/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala
+15
-15
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
...a/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
+15
-15
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
...nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
+42
-37
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
+133
-63
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
+23
-22
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+19
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+29
-28
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
+41
-33
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+26
-23
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+22
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
+18
-17
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+130
-118
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+35
-33
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
+42
-41
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+95
-90
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
+22
-21
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
+24
-23
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
.../scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
+27
-26
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+20
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+18
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
...ns/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+36
-31
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+24
-22
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
+25
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+42
-38
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+38
-34
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
+22
-21
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+15
-14
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+27
-23
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
+23
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+19
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+72
-46
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+29
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
+22
-21
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+130
-119
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+147
-127
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+27
-26
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+21
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+41
-40
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
.../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
+31
-30
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
+20
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+43
-34
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
+32
-31
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+31
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
.../lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
...l/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
+20
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
.../scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
+49
-44
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
...scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
+124
-118
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
.../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
+22
-21
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
...a/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
+22
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala
+35
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala
+29
-26
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
+14
-14
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
+18
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+49
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
+28
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+18
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+37
-36
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+28
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
...l/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
+75
-66
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
...sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
+26
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
+34
-29
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
+44
-33
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+13
-13
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
+30
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
+19
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
+19
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
+22
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
+21
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCAssessSignificancePlot.scala
...biopet/extensions/freec/FreeCAssessSignificancePlot.scala
+16
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
...a/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
+14
-14
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
...a/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
+19
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
...scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
+21
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
+22
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala
...n/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala
+121
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
...la/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
+39
-38
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
+19
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+60
-53
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+28
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
+21
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
+18
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+39
-39
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
...in/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
+30
-30
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
...sc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
...c/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
+16
-17
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
...c/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
...c/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala
...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
...umc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
+20
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
.../sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
+18
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
.../sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
+18
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+39
-32
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala
+26
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
...nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
+20
-19
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
+35
-28
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+36
-28
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectHsMetrics.scala
...lumc/sasc/biopet/extensions/picard/CollectHsMetrics.scala
+32
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+35
-28
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
...asc/biopet/extensions/picard/CollectMultipleMetrics.scala
+82
-47
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+49
-42
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
.../biopet/extensions/picard/CollectTargetedPcrMetrics.scala
+40
-32
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
+28
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CreateSequenceDictionary.scala
...c/biopet/extensions/picard/CreateSequenceDictionary.scala
+23
-22
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
...l/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
+18
-17
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+49
-34
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+32
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/NormalizeFasta.scala
...l/lumc/sasc/biopet/extensions/picard/NormalizeFasta.scala
+27
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+83
-60
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+27
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+34
-32
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+26
-22
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
+26
-22
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+78
-72
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+34
-31
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
...ala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
+56
-50
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
...nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
+42
-41
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
...a/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
+26
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
...nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
+25
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
+39
-31
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
.../sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
+36
-33
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
...scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
+86
-80
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
...ala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
+26
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
...mc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
+50
-47
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
...la/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
...mc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
+21
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
+21
-20
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
+30
-26
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
+24
-23
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
+14
-14
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
+24
-23
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
.../nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
.../lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+19
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+28
-27
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
+27
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
+26
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
...in/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
+14
-14
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala
...la/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala
+24
-23
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+25
-25
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
...a/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
+15
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
...cala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
+14
-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
...c/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
+37
-30
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
+17
-17
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
...scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
+24
-23
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
...scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
+25
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
...main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
+18
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
+25
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
...cala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
+18
-17
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
...umc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
+16
-16
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
...a/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
+18
-17
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
...n/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
+16
-16
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala
...t/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala
+15
-15
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
...t/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
+16
-16
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala
...est/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala
+15
-15
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+16
-16
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
...scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
+16
-16
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
...rc/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
+25
-19
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
...test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
+149
-86
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala
...c/sasc/biopet/extensions/VariantEffectPredictorTest.scala
+15
-15
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/XhmmTest.scala
.../test/scala/nl/lumc/sasc/biopet/extensions/XhmmTest.scala
+15
-15
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
...lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
+32
-24
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
...opet/extensions/picard/CollectInsertSizeMetricsTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
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biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
...la/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
.../nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
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-17
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
...c/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
.../nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
...la/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
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-24
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
...mc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
.../scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
...a/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
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-20
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala
.../nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala
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-18
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateVcf.scala
...la/nl/lumc/sasc/biopet/extensions/tools/ValidateVcf.scala
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-18
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
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-38
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
...scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala
.../nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala
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-18
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
...ala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
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-23
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
.../nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
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-16
biopet-tools-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala
.../nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala
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-33
biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
...ain/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
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-47
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
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-52
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
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-23
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
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-30
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
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-20
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
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-47
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
...cala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
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-31
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala
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-25
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
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-24
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
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-51
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
...in/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
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-25
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
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-37
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
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-37
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
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-19
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
.../scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
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-61
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
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-32
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
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-24
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
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-62
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
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-53
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
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-25
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
.../main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
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-66
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
...main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
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-27
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToConfig.scala
.../scala/nl/lumc/sasc/biopet/tools/SamplesTsvToConfig.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
...ls/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
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-34
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
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-39
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
.../main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateVcf.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/ValidateVcf.scala
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-24
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
...s/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
...n/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
.../scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
...main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala
...a/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala
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-27
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
...l/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/SampleStats.scala
...cala/nl/lumc/sasc/biopet/tools/vcfstats/SampleStats.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/SampleToSampleStats.scala
...lumc/sasc/biopet/tools/vcfstats/SampleToSampleStats.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
...main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
...n/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala
...la/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
...la/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala
...est/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
.../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssemblyTest.scala
.../nl/lumc/sasc/biopet/tools/DownloadNcbiAssemblyTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqFilterTest.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
.../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/GensToVcfTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala
.../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
...est/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/PrefixFastqTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
.../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
...rc/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SnptestToVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
...st/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ValidateFastqTest.scala
...t/scala/nl/lumc/sasc/biopet/tools/ValidateFastqTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ValidateVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
.../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
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
.../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
...ala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.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
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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-utils/src/main/scala/nl/lumc/sasc/biopet/package.scala
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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/BiopetExecutable.scala
...in/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.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
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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/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/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
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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
...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/process/AsyncProcess.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
...in/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
...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
...la/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
...ain/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
...cala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
...n/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
...cala/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
...c/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
...est/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/IoUtilsTest.scala
...rc/test/scala/nl/lumc/sasc/biopet/utils/IoUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
...rc/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala
.../src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/VcfUtilsTest.scala
...c/test/scala/nl/lumc/sasc/biopet/utils/VcfUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
...t/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
...la/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
...a/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
.../lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
...a/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
...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
.../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
.../nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
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carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
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carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
...scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
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carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
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external-example/src/main/scala/org/example/group/ExecutableExample.scala
.../src/main/scala/org/example/group/ExecutableExample.scala
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external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
...in/scala/org/example/group/pipelines/BiopetPipeline.scala
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external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala
...ain/scala/org/example/group/pipelines/HelloPipeline.scala
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external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
...ala/org/example/group/pipelines/MultisamplePipeline.scala
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external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
...in/scala/org/example/group/pipelines/SimplePipeline.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/AdapterSequence.scala
...umc/sasc/biopet/pipelines/flexiprep/AdapterSequence.scala
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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
...la/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
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
...l/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
...umc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
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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/GearsCentrifuge.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/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/GearsKrakenTest.scala
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosedTest.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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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/GenerateIndexes.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
...iopet/pipelines/generateindexes/DownloadGenomesTest.scala
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generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfigTest.scala
...sc/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/GentrapReport.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
...c/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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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
.../biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
.../biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
.../sasc/biopet/pipelines/gentrap/measures/Measurement.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
...c/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
...lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
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gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
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gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
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gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
...mc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
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gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala
.../sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala
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gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Spec.scala
.../nl/lumc/sasc/biopet/pipelines/gwastest/impute/Spec.scala
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gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
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gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
...asc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
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+23
-17
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
...c/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
+29
-27
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala
...lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala
+17
-16
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
.../sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
+16
-16
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
...mc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
+27
-22
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
...umc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
+41
-27
kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
+34
-34
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+101
-75
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+45
-30
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
...mc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+113
-75
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+256
-122
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
.../biopet/pipelines/mapping/scripts/TophatRecondition.scala
+18
-18
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/template/MultiSampleMapping.scala
...iopet/pipelines/mapping/template/MultiSampleMapping.scala
+33
-21
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+44
-36
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
...asc/biopet/pipelines/mapping/MultisampleMappingTest.scala
+98
-67
sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+78
-47
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
+48
-44
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/CheckValidateVcf.scala
...l/lumc/sasc/biopet/pipelines/shiva/CheckValidateVcf.scala
+18
-18
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+133
-82
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+114
-58
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+37
-27
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingReport.scala
...mc/sasc/biopet/pipelines/shiva/ShivaSvCallingReport.scala
+69
-32
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+64
-44
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
...c/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
+29
-18
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+14
-14
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
+15
-14
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+20
-19
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
...lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
+17
-17
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala
+19
-17
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
...sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
+14
-14
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
...pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
+16
-16
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
...asc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
+14
-14
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCaller.scala
...opet/pipelines/shiva/variantcallers/HaplotypeCaller.scala
+26
-25
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
...ipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
+26
-24
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
.../pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
+43
-33
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
...c/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
+23
-21
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyper.scala
...pet/pipelines/shiva/variantcallers/UnifiedGenotyper.scala
+26
-24
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
...pelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
+26
-24
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
...biopet/pipelines/shiva/variantcallers/Variantcaller.scala
+18
-19
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
...pelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+17
-17
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
...lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+57
-52
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+87
-67
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+85
-47
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
...elines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
+22
-20
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
...scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
+30
-29
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala
...nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala
+19
-17
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/measures/FragmentsPerSmallRna.scala
...pet/pipelines/tinycap/measures/FragmentsPerSmallRna.scala
+23
-17
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
+40
-44
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterImport.scala
...sc/biopet/pipelines/toucan/ManweActivateAfterImport.scala
+28
-23
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
.../biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
+23
-22
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+84
-63
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
+22
-19
No files found.
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
e5bbde4d
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.WigToBigWig
import
nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
import
org.broadinstitute.gatk.queue.QScript
/**
* Pipeline to create BigWigle files from a bam file
*
* Created by pjvan_thof on 1/29/15.
*/
* Pipeline to create BigWigle files from a bam file
*
* Created by pjvan_thof on 1/29/15.
*/
class
Bam2Wig
(
val
parent
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
...
...
@@ -70,4 +70,4 @@ object Bam2Wig extends PipelineCommand {
bamToBigWig
.
bamFile
=
bamFile
bamToBigWig
}
}
\ No newline at end of file
}
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
View file @
e5bbde4d
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.function.InProcessFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
/**
* Class to extract chrom.sizes files from a bam file
*
* Created by pjvan_thof on 1/29/15.
*/
* Class to extract chrom.sizes files from a bam file
*
* Created by pjvan_thof on 1/29/15.
*/
class
BamToChromSizes
(
val
parent
:
Configurable
)
extends
InProcessFunction
with
Configurable
{
@Input
var
bamFile
:
File
=
_
...
...
bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
View file @
e5bbde4d
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.File
...
...
@@ -24,8 +24,8 @@ import org.testng.annotations.Test
import
scala.io.Source
/**
* Created by pjvanthof on 09/05/16.
*/
* Created by pjvanthof on 09/05/16.
*/
class
BamToChromSizesTest
extends
TestNGSuite
with
Matchers
{
private
def
resourcePath
(
p
:
String
)
:
String
=
{
Paths
.
get
(
getClass
.
getResource
(
p
).
toURI
).
toString
...
...
@@ -39,6 +39,7 @@ class BamToChromSizesTest extends TestNGSuite with Matchers {
bamToChromSizes
.
chromSizesFile
=
File
.
createTempFile
(
"chrom."
,
".sizes"
)
bamToChromSizes
.
chromSizesFile
.
deleteOnExit
()
bamToChromSizes
.
run
()
Source
.
fromFile
(
bamToChromSizes
.
chromSizesFile
).
getLines
().
toList
shouldBe
List
(
"chrQ\t10000"
,
"chrR\t10000"
)
Source
.
fromFile
(
bamToChromSizes
.
chromSizesFile
).
getLines
().
toList
shouldBe
List
(
"chrQ\t10000"
,
"chrR\t10000"
)
}
}
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
e5bbde4d
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.File
import
nl.lumc.sasc.biopet.core.annotations.
{
AnnotationRefFlat
,
RibosomalRefFlat
}
import
nl.lumc.sasc.biopet.core.annotations.
{
AnnotationRefFlat
,
RibosomalRefFlat
}
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
,
BedtoolsSort
}
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
,
BedtoolsSort
}
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.extensions.tools.
{
BamStats
,
BiopetFlagstat
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
BamStats
,
BiopetFlagstat
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.intervals.BedCheck
import
org.broadinstitute.gatk.queue.QScript
class
BamMetrics
(
val
parent
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
with
Reference
with
TargetRegions
with
AnnotationRefFlat
with
RibosomalRefFlat
{
class
BamMetrics
(
val
parent
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
with
Reference
with
TargetRegions
with
AnnotationRefFlat
with
RibosomalRefFlat
{
def
this
()
=
this
(
null
)
...
...
@@ -44,30 +45,32 @@ class BamMetrics(val parent: Configurable) extends QScript
override
def
defaults
=
Map
(
"bedtoolscoverage"
->
Map
(
"sorted"
->
true
))
/** returns files to store in summary */
def
summaryFiles
=
Map
(
"reference"
->
referenceFasta
(),
"input_bam"
->
inputBam
)
++
ampliconBedFile
.
map
(
"amplicon"
->
_
).
toMap
++
ampliconBedFile
.
map
(
x
=>
"roi_"
+
x
.
getName
.
stripSuffix
(
".bed"
)
->
x
).
toMap
def
summaryFiles
=
Map
(
"reference"
->
referenceFasta
(),
"input_bam"
->
inputBam
)
++
ampliconBedFile
.
map
(
"amplicon"
->
_
).
toMap
++
ampliconBedFile
.
map
(
x
=>
"roi_"
+
x
.
getName
.
stripSuffix
(
".bed"
)
->
x
).
toMap
/** return settings */
def
summarySettings
=
Map
(
"amplicon_name"
->
ampliconBedFile
.
collect
{
case
x
=>
x
.
getName
.
stripSuffix
(
".bed"
)
},
"roi_name"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)))
def
summarySettings
=
Map
(
"amplicon_name"
->
ampliconBedFile
.
collect
{
case
x
=>
x
.
getName
.
stripSuffix
(
".bed"
)
},
"roi_name"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)))
override
def
reportClass
=
{
val
bammetricsReport
=
new
BammetricsReport
(
this
)
bammetricsReport
.
outputDir
=
new
File
(
outputDir
,
"report"
)
bammetricsReport
.
summaryDbFile
=
summaryDbFile
bammetricsReport
.
args
=
if
(
libId
.
isDefined
)
Map
(
"sampleId"
->
sampleId
.
getOrElse
(
"."
),
"libId"
->
libId
.
getOrElse
(
"."
))
else
Map
(
"sampleId"
->
sampleId
.
getOrElse
(
"."
))
bammetricsReport
.
args
=
if
(
libId
.
isDefined
)
Map
(
"sampleId"
->
sampleId
.
getOrElse
(
"."
),
"libId"
->
libId
.
getOrElse
(
"."
))
else
Map
(
"sampleId"
->
sampleId
.
getOrElse
(
"."
))
Some
(
bammetricsReport
)
}
/** executed before script */
def
init
()
:
Unit
=
{
inputFiles
:+=
new
InputFile
(
inputBam
)
ampliconBedFile
.
foreach
(
BedCheck
.
checkBedFileToReference
(
_
,
referenceFasta
(),
biopetError
=
true
))
ampliconBedFile
.
foreach
(
BedCheck
.
checkBedFileToReference
(
_
,
referenceFasta
(),
biopetError
=
true
))
roiBedFiles
.
foreach
(
BedCheck
.
checkBedFileToReference
(
_
,
referenceFasta
(),
biopetError
=
true
))
}
...
...
@@ -129,13 +132,19 @@ class BamMetrics(val parent: Configurable) extends QScript
ampBedToInterval
.
isIntermediate
=
true
add
(
ampBedToInterval
)
val
chsMetrics
=
CollectHsMetrics
(
this
,
inputBam
,
List
(
ampIntervals
),
ampIntervals
::
roiIntervals
.
map
(
_
.
intervals
),
outputDir
)
val
chsMetrics
=
CollectHsMetrics
(
this
,
inputBam
,
List
(
ampIntervals
),
ampIntervals
::
roiIntervals
.
map
(
_
.
intervals
),
outputDir
)
add
(
chsMetrics
)
addSummarizable
(
chsMetrics
,
"hs_metrics"
)
val
pcrMetrics
=
CollectTargetedPcrMetrics
(
this
,
inputBam
,
ampIntervals
,
ampIntervals
::
roiIntervals
.
map
(
_
.
intervals
),
outputDir
)
val
pcrMetrics
=
CollectTargetedPcrMetrics
(
this
,
inputBam
,
ampIntervals
,
ampIntervals
::
roiIntervals
.
map
(
_
.
intervals
),
outputDir
)
add
(
pcrMetrics
)
addSummarizable
(
pcrMetrics
,
"targeted_pcr_metrics"
)
...
...
@@ -145,36 +154,48 @@ class BamMetrics(val parent: Configurable) extends QScript
// Create stats and coverage plot for each bed/interval file
val
allIntervalNames
=
(
roiIntervals
++
ampIntervals
).
map
(
_
.
bed
.
getName
)
if
(
allIntervalNames
.
size
!=
allIntervalNames
.
toSet
.
size
)
{
logger
.
warn
(
"There are multiple region files with the same name. Metric values might get overwritten"
)
logger
.
warn
(
"There are multiple region files with the same name. Metric values might get overwritten"
)
}
for
(
intervals
<-
roiIntervals
++
ampIntervals
)
{
val
targetName
=
intervals
.
bed
.
getName
.
stripSuffix
(
".bed"
)
val
targetDir
=
new
File
(
outputDir
,
targetName
)
val
biStrict
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
val
biStrict
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.strict.sam"
),
minOverlap
=
config
(
"strict_intersect_overlap"
,
default
=
1.0
))
minOverlap
=
config
(
"strict_intersect_overlap"
,
default
=
1.0
)
)
val
biopetFlagstatStrict
=
BiopetFlagstat
(
this
,
biStrict
.
output
,
targetDir
)
addSummarizable
(
biopetFlagstatStrict
,
targetName
+
"_flagstats_strict"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biStrict
,
biopetFlagstatStrict
)))
val
biLoose
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
val
biLoose
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.loose.sam"
),
minOverlap
=
config
(
"loose_intersect_overlap"
,
default
=
0.01
))
minOverlap
=
config
(
"loose_intersect_overlap"
,
default
=
0.01
)
)
val
biopetFlagstatLoose
=
BiopetFlagstat
(
this
,
biLoose
.
output
,
targetDir
)
addSummarizable
(
biopetFlagstatLoose
,
targetName
+
"_flagstats_loose"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biLoose
,
biopetFlagstatLoose
)))
val
sortedBed
=
BamMetrics
.
sortedbedCache
.
getOrElse
(
intervals
.
bed
,
{
val
sorter
=
new
BedtoolsSort
(
this
)
sorter
.
input
=
intervals
.
bed
sorter
.
output
=
swapExt
(
targetDir
,
intervals
.
bed
,
".bed"
,
".sorted.bed"
)
add
(
sorter
)
BamMetrics
.
sortedbedCache
+=
intervals
.
bed
->
sorter
.
output
sorter
.
output
})
val
sortedBed
=
BamMetrics
.
sortedbedCache
.
getOrElse
(