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biopet.biopet
Commits
2c9c7c06
Commit
2c9c7c06
authored
Mar 29, 2017
by
Peter van 't Hof
Committed by
GitHub
Mar 29, 2017
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Merge pull request #45 from biopet/epic-summary_reformat
Epic summary reformat
parents
3c83710e
9ab675f8
Changes
362
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362 changed files
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3547 additions
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1917 deletions
+3547
-1917
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+1
-1
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+1
-1
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
+29
-22
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
...ces/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
+25
-29
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
...c/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
+29
-39
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
+24
-28
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
+27
-29
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
.../lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
+26
-29
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
+23
-26
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
+25
-29
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+2
-9
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+142
-174
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
+1
-1
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+13
-11
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+1
-3
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
+20
-11
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
...resources/nl/lumc/sasc/biopet/core/report/executables.ssp
+9
-9
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/fileModules.ssp
...resources/nl/lumc/sasc/biopet/core/report/fileModules.ssp
+25
-0
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/files.ssp
.../main/resources/nl/lumc/sasc/biopet/core/report/files.ssp
+42
-0
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
...sources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
+8
-5
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
...c/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
+2
-2
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
...n/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
+20
-8
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
...resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
+7
-4
biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
...resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
+0
-40
biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
...main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
+0
-40
biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
.../resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
+0
-35
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+2
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+20
-11
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+22
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+2
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
...ain/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
+2
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+4
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
...in/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
...sc/biopet/core/extensions/PythonCommandLineFunction.scala
+6
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
...mc/sasc/biopet/core/report/MultisampleReportBuilder.scala
+14
-8
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+56
-19
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
...scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
+3
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+74
-33
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+116
-97
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
.../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
+2
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
...a/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
...ala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
...c/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
...scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
+3
-3
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
...test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
.../nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala
...asc/biopet/core/report/MultisampleReportBuilderTest.scala
+24
-3
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
...a/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
+21
-4
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
...nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
+108
-82
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
.../scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
...ns/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
.../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
+2
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
.../lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
...l/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
.../scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
...scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
.../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
...a/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
...l/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
...sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
...in/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCAssessSignificancePlot.scala
...biopet/extensions/freec/FreeCAssessSignificancePlot.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
...a/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
...a/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
.../lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala
.../lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala
.../lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
...la/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
...nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala
...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
...a/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
.../nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
...cala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
.../sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
.../nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
...l/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
...ala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
...umc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
...scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala
...n/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
...la/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
...sc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
...c/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
...c/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
...c/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala
...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
...umc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
.../sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
.../sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
...nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectHsMetrics.scala
...lumc/sasc/biopet/extensions/picard/CollectHsMetrics.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
...asc/biopet/extensions/picard/CollectMultipleMetrics.scala
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-15
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
.../biopet/extensions/picard/CollectTargetedPcrMetrics.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CreateSequenceDictionary.scala
...c/biopet/extensions/picard/CreateSequenceDictionary.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
...l/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/NormalizeFasta.scala
...l/lumc/sasc/biopet/extensions/picard/NormalizeFasta.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
...ala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
...nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
...a/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
...nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
.../sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
...scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
...ala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
...mc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
...mc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
.../nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
.../lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala
...la/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
...a/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
...c/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
...scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
...scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
...cala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
...umc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
...a/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
...n/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
...t/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
...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
...umc/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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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
...a/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
...a/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
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
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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
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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
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
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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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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateVcf.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
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biopet-tools-extensions/src/main/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/VcfWithVcf.scala
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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
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
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biopet-utils/pom.xml
biopet-utils/pom.xml
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biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
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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/Configurable.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/ScatterPlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/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
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biopet-utils/src/main/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
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/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/summary/db/SummaryDbTest.scala
.../nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
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-0
carp/src/main/resources/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp
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-5
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
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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/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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-3
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/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
.../sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
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-47
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
...c/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
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flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
...l/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
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-10
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
.../sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
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-6
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
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-44
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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-37
flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
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-16
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
...ources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
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-7
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
.../nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
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-8
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
...la/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/ExtractUnmappedReads.scala
...mc/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
...nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
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-4
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
...l/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
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-29
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
...a/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/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
...sc/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
...sc/biopet/pipelines/generateindexes/GenerateIndexes.scala
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generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.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
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
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gentrap/src/main/scala/nl/lumc/sasc/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/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
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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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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
.../sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
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kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
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mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
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mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp
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mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp
.../nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
.../biopet/pipelines/mapping/scripts/TophatRecondition.scala
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mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
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mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
...asc/biopet/pipelines/mapping/MultisampleMappingTest.scala
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pom.xml
pom.xml
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sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
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-3
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
+20
-11
shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
...es/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
+23
-12
shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
...ources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
+31
-13
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+11
-8
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+37
-55
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+1
-4
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+1
-4
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
...c/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
...sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
...pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
...asc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCaller.scala
...opet/pipelines/shiva/variantcallers/HaplotypeCaller.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
...ipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
.../pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
...c/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyper.scala
...pet/pipelines/shiva/variantcallers/UnifiedGenotyper.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
...pelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
...pelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+1
-1
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
...lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+32
-14
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+22
-10
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+20
-11
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
...scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
+2
-4
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala
...nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala
+1
-13
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/measures/FragmentsPerSmallRna.scala
...pet/pipelines/tinycap/measures/FragmentsPerSmallRna.scala
+1
-1
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
+17
-14
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+2
-4
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
+29
-9
No files found.
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
2c9c7c06
...
...
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.queue.QScript
*
* Created by pjvan_thof on 1/29/15.
*/
class
Bam2Wig
(
val
roo
t
:
Configurable
)
extends
QScript
with
BiopetQScript
{
class
Bam2Wig
(
val
paren
t
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
@Input
(
doc
=
"Input bam file"
,
required
=
true
)
...
...
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
View file @
2c9c7c06
...
...
@@ -28,7 +28,7 @@ import scala.collection.JavaConversions._
*
* Created by pjvan_thof on 1/29/15.
*/
class
BamToChromSizes
(
val
roo
t
:
Configurable
)
extends
InProcessFunction
with
Configurable
{
class
BamToChromSizes
(
val
paren
t
:
Configurable
)
extends
InProcessFunction
with
Configurable
{
@Input
var
bamFile
:
File
=
_
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @
2c9c7c06
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[
String
] = None %>
<%@ var libId: Option[
String
] = None %>
<%@ var summary: Summary
Db
%>
<%@ var sampleId: Option[
Int
] = None %>
<%@ var libId: Option[
Int
] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
<br/>
...
...
@@ -69,24 +69,31 @@
<th>(%)</th>
</tr></thead>
<tbody>
#for (sample <- samples.
toList.sorted
)
#for (sample <- samples.
sortBy(_.name)
)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List(
""
)
case (Some(
libId), _) => List(libId.toString).sorted
case _ =>
summary.libraries(sample).toList.sorted
val libs
: List[Option[Int]]
= (libId, sampleLevel) match {
case (_, true) => List(
None
)
case (Some(
_), _) => List(libId)
case _ =>
Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
}/index.html">${sampl
e}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
.name}/index.html">${sample.nam
e}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample
}/Libraries/${libId}/index.html">${libId
}</a></td> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample
.name}/Libraries/${libName}/index.html">${libName
}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val total = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
val secondary = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long]
val statsPaths = Map(
"All" -> List("flagstats", "All"),
"Mapped" -> List("flagstats", "Mapped"),
"Duplicates" -> List("flagstats", "Duplicates"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
val total = results("All").getOrElse(0L).asInstanceOf[Long]
val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long]
val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long]
val secondary = results("NotPrimaryAlignment").getOrElse(0L).asInstanceOf[Long]
}#
<td>${total}</td>
<td>${mapped}</td>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
View file @
2c9c7c06
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
...
...
@@ -42,7 +40,7 @@
#end
#if (showPlot)
#{ BammetricsReport.clippingPlot(outputDir, "clipping", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.clippingPlot(outputDir, "clipping", summary, !sampleLevel, sampleId = sampleId, lib
rary
Id = libId) }#
<div class="panel-body">
<img src="clipping.png" class="img-responsive" />
...
...
@@ -71,27 +69,25 @@
#end
</tr></thead>
<tbody>
#for (sample <- samples.
toList.sorted
)
#for (sample <- samples.
sortBy(_.name)
)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List(
""
)
case (Some(
libId), _) => List(libId.toString
)
case _ =>
summary.libraries(sample
).toList
val libs
: List[Option[Int]]
= (libId, sampleLevel) match {
case (_, true) => List(
None
)
case (Some(
_), _) => List(libId
)
case _ =>
Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)
).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
}/index.html">${sampl
e}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
.name}/index.html">${sample.nam
e}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample
}/Libraries/${libId}/index.html">${libId
}</a></td> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample
.name}/Libraries/${libName}/index.html">${libName
}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List("bamstats", "clipping", "general", field)):_*).getOrElse("N/A")
}
val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap
val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}#
#for (
value <- fieldValue
s)
<td>${
value
}</td>
#for (
field <- field
s)
<td>${
results(field)
}</td>
#end
</tr>
#end
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
View file @
2c9c7c06
#import(nl.lumc.sasc.biopet.utils.IoUtils)
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = true %>
<%@ var
rootPath: String
%>
<%@ var
libId: Option[Int] = None
%>
<%@ var outputDir: File %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var target: Option[String] %>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
#{
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
<table class="table">
<thead><tr>
<th>sample</th>
<th>mean</th>
<th>median</th>
<th>max</th>
<th>horizontal</th>
<th>frac min 10x</th>
<th>frac min 20x</th>
<th>frac min 30x</th>
<th>frac min 40x</th>
<th>frac min 50x</th>
#for (field <- fields)
<th>${field}</th>
#end
</tr></thead>
<tbody>
#for (sample <- samples.
toList.sorted
)
#for (sample <- samples.
sortBy(_.name)
)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List(""
)
case (Some(libId), _) => List(libId.toString
)
case _ => summary.libraries(sample
).toList
val libs
: List[Option[Int]]
= (libId, sampleLevel) match {
case (_, true) => List(None
)
case (Some(_), _) => List(libId
)
case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)
).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
}/index.html">${sampl
e}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
.name}/index.html">${sample.nam
e}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
val moduleName = target.get + "_cov_stats"
val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
val values = summary.getStatKeys(runId, PipelineName(metricsTag), ModuleName(moduleName), SampleId(sample.id), libId.map(LibraryId).getOrElse(NoLibrary), statsPaths)
}#
<td>${summary.getValue((prefixPath ::: "mean" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "median" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "max" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "horizontal" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_10x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_20x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_30x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_40x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_50x" :: Nil):_*)}</td>
#for (field <- fields)
<th>${values(field)}</th>
#end
</tr>
#end
#end
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
View file @
2c9c7c06
#import(nl.lumc.sasc.biopet.utils.IoUtils)
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[
String
] %>
<%@ var libId: Option[
String
] = None %>
<%@ var summary: Summary
Db
%>
<%@ var sampleId: Option[
Int
] %>
<%@ var libId: Option[
Int
] = None %>
<%@ var outputDir: File %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var target: Option[String] %>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
#{
val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target.get + "_cov_stats", "plot", "path")
.getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)
val moduleName = target.get + "_cov_stats"
val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
val plotFile = Await.result(summary.getFile(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), "plot"), Duration.Inf)
val originalPlot = new File(plotFile.get.path)
val plot = new File(outputDir, target.get + "_cov_stats.png")
val values = summary.getValue(sampleId, libId, metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
.getOrElse(throw new IllegalArgumentException("No plot found in summary")).asInstanceOf[Map[String, Any]]
val values = summary.getStatKeys(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), statsPaths)
if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
}#
<img src="${plot.getName}">
<table class="table">
<thead><tr>
<th>mean</th>
<th>median</th>
<th>max</th>
<th>horizontal</th>
<th>frac min 10x</th>
<th>frac min 20x</th>
<th>frac min 30x</th>
<th>frac min 40x</th>
<th>frac min 50x</th>
#for (field <- fields)
<th>${field}</th>
#end
</tr></thead>
<tbody>
<tr>
<td>${values.get("mean")}</td>
<td>${values.get("median")}</td>
<td>${values.get("max")}</td>
<td>${values.get("horizontal")}</td>
<td>${values.get("frac_min_10x")}</td>
<td>${values.get("frac_min_20x")}</td>
<td>${values.get("frac_min_30x")}</td>
<td>${values.get("frac_min_40x")}</td>
<td>${values.get("frac_min_50x")}</td>
#for (field <- fields)
<th>${values(field)}</th>
#end
</tr>
</tbody>
</table>
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @
2c9c7c06
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var sampleLevel: Boolean = false %>
...
...
@@ -14,13 +17,9 @@
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
...
...
@@ -43,7 +42,7 @@
#end
#if (showPlot)
#{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, lib
rary
Id = libId) }#
<div class="panel-body">
<img src="insertsize.png" class="img-responsive" />
...
...
@@ -72,28 +71,27 @@
#end
</tr></thead>
<tbody>
#for (sample <- samples.
toList.sorted
)
#for (sample <- samples.
sortBy(_.name)
)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List(
""
)
case (Some(
libId), _) => List(libId.toString
)
case _ =>
summary.libraries(sample
).toList
val libs
: List[Option[Int]]
= (libId, sampleLevel) match {
case (_, true) => List(
None
)
case (Some(
_), _) => List(libId
)
case _ =>
Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)
).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
}/index.html">${sampl
e}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
.name}/index.html">${sample.nam
e}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse("N/A")
}
}#
#for (value <- fieldValues)
<td>${value}</td>
#end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val results = summary.getStatKeys(runId, "bammetrics", "CollectInsertSizeMetrics", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
#end
</tr>
</tr>
#end
#end
...
...