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biopet.biopet
Commits
9812237c
Commit
9812237c
authored
Jul 01, 2015
by
Peter van 't Hof
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493 additions
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526 deletions
+493
-526
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
...mc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
...l/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
...biopet/extensions/gatk/broad/RealignerTargetCreator.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
...mc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
.../sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
.../lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
+1
-0
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
+1
-0
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
+2
-2
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+2
-3
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+7
-9
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
...sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
+1
-2
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+5
-4
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+1
-1
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+2
-2
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+4
-4
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+0
-1
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+3
-2
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+6
-5
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+3
-3
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+2
-2
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+4
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
...k/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+1
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
...n/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
+1
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
...main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+7
-7
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+8
-11
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
...k/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+3
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+1
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
+2
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
...rk/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+2
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
...mc/sasc/biopet/extensions/PythonCommandLineFunction.scala
+3
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
...c/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+2
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+3
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
+3
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+3
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+1
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+0
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
+0
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
...in/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
+3
-6
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
+1
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
+1
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+3
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+0
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
...asc/biopet/extensions/picard/CollectMultipleMetrics.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
.../biopet/extensions/picard/CollectTargetedPcrMetrics.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
...l/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
+1
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+4
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+1
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
.../scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
+4
-7
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+3
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+4
-5
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
.../lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
...mc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
.../nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
+1
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
...c/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala
...cala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala
+1
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
...ain/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala
...rc/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
+4
-6
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+5
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+4
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+4
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
...main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
+6
-13
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+4
-7
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+7
-9
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+10
-12
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+5
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+6
-6
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+3
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
...main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+5
-6
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+5
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+6
-5
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
...in/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
+3
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
...rk/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
+7
-11
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+7
-6
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+7
-7
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
+3
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+2
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+8
-8
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+7
-13
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+5
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
...rk/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
...k/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
+1
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
...st/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
...ala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
+0
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
...la/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+0
-2
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+2
-3
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
...scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
+2
-2
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
...rc/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
+1
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
...la/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
...a/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
+2
-3
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
+2
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
...est/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
+2
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
...rc/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
...c/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
+2
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
...c/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
+0
-2
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
...test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
...t/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
+8
-8
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
+4
-11
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
...est/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+2
-2
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+3
-5
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+6
-7
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+4
-3
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
...cala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+2
-3
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+4
-7
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+3
-3
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
...la/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+1
-0
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+4
-6
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+1
-1
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala
+5
-6
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
...umc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
+1
-2
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+12
-11
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+2
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
.../biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
+4
-4
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
...t/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
+1
-3
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+4
-9
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
...l/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
+2
-4
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
...nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
+1
-1
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+10
-12
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
.../biopet/pipelines/mapping/scripts/TophatRecondition.scala
+0
-1
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+7
-8
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+2
-8
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+1
-1
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+3
-3
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+3
-2
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+4
-6
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+2
-2
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+3
-3
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+1
-2
public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+3
-6
No files found.
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
AnalyzeCovariates
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
AnalyzeCovariates
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
ApplyRecalibration
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
ApplyRecalibration
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
BaseRecalibrator
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
CombineGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineGVCFs
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
CombineVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineVariants
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
View file @
9812237c
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetJavaCommandLineFunction
}
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
Reference
}
import
org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait
GatkGeneral
extends
CommandLineGATK
with
BiopetJavaCommandLineFunction
with
Reference
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
GenotypeGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
GenotypeGVCFs
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
IndelRealigner
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
IndelRealigner
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
PrintReads
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
PrintReads
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
RealignerTargetCreator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
RealignerTargetCreator
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
SelectVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
SelectVariants
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
VariantAnnotator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantAnnotator
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
VariantEval
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantEval
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
View file @
9812237c
...
...
@@ -6,6 +6,7 @@
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
View file @
9812237c
...
...
@@ -5,10 +5,10 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
}
import
scala.util.Random
class
GatkBenchmarkGenotyping
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
View file @
9812237c
...
...
@@ -5,11 +5,10 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
SelectVariants
,
GenotypeGVCFs
}
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
GenotypeGVCFs
,
SelectVariants
}
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
class
GatkGenotyping
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
9812237c
...
...
@@ -5,20 +5,18 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.
{
MultiSampleQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
CombineVariants
,
CombineGVCFs
}
import
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
scala.collection.JavaConversions._
import
nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
CombineGVCFs
,
CombineVariants
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
SamToFastq
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
}
import
scala.collection.JavaConversions._
class
GatkPipeline
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
with
SummaryQScript
{
qscript
=>
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
View file @
9812237c
...
...
@@ -5,8 +5,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.BiopetQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
ApplyRecalibration
,
VariantAnnotator
,
VariantRecalibrator
}
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
9812237c
...
...
@@ -5,17 +5,18 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.tools.
{
VcfStats
,
MpileupToVcf
,
VcfFilter
,
MergeAlleles
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.tools.
{
MergeAlleles
,
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
}
import
scala.collection.SortedMap
import
scala.language.reflectiveCalls
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
9812237c
...
...
@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
Shiva
VariantcallingTrait
,
Shiva
Trait
}
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
Shiva
Trait
,
ShivaVariantcalling
Trait
}
import
org.broadinstitute.gatk.queue.QScript
/**
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
9812237c
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.
{
File
OutputStream
,
File
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.config.Config
...
...
@@ -17,7 +17,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
Test
,
DataProvider
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
/**
* Created by pjvan_thof on 3/2/15.
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
9812237c
...
...
@@ -5,19 +5,19 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.
{
File
OutputStream
,
File
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.config.Config
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
UnifiedGenotyper
,
HaplotypeCall
er
}
import
nl.lumc.sasc.biopet.tools.
{
VcfStats
,
MpileupToVcf
,
VcfFilter
}
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
HaplotypeCaller
,
UnifiedGenotyp
er
}
import
nl.lumc.sasc.biopet.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
,
AfterClass
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
import
scala.collection.mutable.ListBuffer
...
...
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
9812237c
...
...
@@ -22,7 +22,6 @@ 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
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvan_thof on 1/29/15.
...
...
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
View file @
9812237c
...
...
@@ -15,12 +15,13 @@
*/
package
nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.
{
PrintWriter
,
File
}
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.function.InProcessFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
/**
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
9812237c
...
...
@@ -15,16 +15,17 @@
*/
package
nl.lumc.sasc.biopet.pipelines.bammetrics
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.scripts.CoverageStats
import
org.broadinstitute.gatk.queue.QScript
import
nl.lumc.sasc.biopet.core.
{
SampleLibraryTag
,
PipelineCommand
}
import
java.io.File
import
nl.lumc.sasc.biopet.tools.BiopetFlagstat
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.scripts.CoverageStats
import
nl.lumc.sasc.biopet.tools.BiopetFlagstat
import
org.broadinstitute.gatk.queue.QScript
class
BamMetrics
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
def
this
()
=
this
(
null
)
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
9812237c
package
nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.
{
PrintWriter
,
File
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilder
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summary
Value
,
Summary
}
import
nl.lumc.sasc.biopet.extensions.rscript.
{
XYPlot
,
StackedBar
Plot
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summary
,
SummaryValue
}
import
nl.lumc.sasc.biopet.extensions.rscript.
{
StackedBarPlot
,
XY
Plot
}
/**
* Created by pjvan_thof on 3/30/15.
...
...
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
9812237c
package
nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.
{
File
OutputStream
,
File
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.config.Config
...
...
@@ -14,7 +14,7 @@ import org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
Test
,
DataProvider
,
AfterClass
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
/**
* Created by pjvan_thof on 4/30/15.
...
...
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
View file @
9812237c
...
...
@@ -21,10 +21,10 @@
package
nl.lumc.sasc.biopet.pipelines.basty
import
java.io.File
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.extensions.
{
RunGubbins
,
Cat
,
Raxml
}
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
ShivaTrait
,
Shiva
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
Shiva
,
ShivaTrait
}
import
nl.lumc.sasc.biopet.tools.BastyGenerateFasta
import
nl.lumc.sasc.biopet.utils.ConfigUtils
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
9812237c
...
...
@@ -15,15 +15,16 @@
*/
package
nl.lumc.sasc.biopet.core
import
java.io.File
import
java.io.
{
File
,
FileInputStream
}
import
java.security.MessageDigest
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.function.CommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.Input
import
scala.collection.mutable
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.util.matching.Regex
import
java.io.FileInputStream
import
java.security.MessageDigest
/** Biopet command line trait to auto check executable and cluster values */
trait
BiopetCommandLineFunctionTrait
extends
CommandLineFunction
with
Configurable
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
View file @
9812237c
...
...
@@ -16,12 +16,12 @@
package
nl.lumc.sasc.biopet.core
import
java.io.
{
PrintWriter
,
StringWriter
}
import
scala.io.Source
import
nl.lumc.sasc.biopet.core.BiopetExecutable._
import
nl.lumc.sasc.biopet.
{
FullVersion
,
LastCommitHash
}
import
org.apache.log4j.Logger
import
nl.lumc.sasc.biopet.
{
FullVersion
,
LastCommitHash
}
import
nl.lumc.sasc.biopet.core.BiopetExecutable._
import
scala.io.Source
/**
* This is the main trait for the biopet executable
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
9812237c
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
org.broadinstitute.gatk.queue.QSettings
import
org.broadinstitute.gatk.queue.function.QFunction
import
org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
import
org.broadinstitute.gatk.utils.commandline.Argument
import
scala.collection.mutable.ListBuffer
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
9812237c
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.
{
Summar
yQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summar
izable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.utils.commandline.Argument
...
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @
9812237c
...
...
@@ -15,12 +15,12 @@
*/
package
nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.config.Config
import
nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
import
org.apache.log4j.
{
PatternLayout
,
WriterAppender
}
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
import
org.apache.log4j.
{
PatternLayout
,
WriterAppender
}
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
/** Wrapper around executable from Queue */
trait
PipelineCommand
extends
MainCommand
with
GatkLogging
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
View file @
9812237c
...
...
@@ -4,6 +4,7 @@ import java.io.File
import
htsjdk.samtools.reference.IndexedFastaSequenceFile
import
nl.lumc.sasc.biopet.core.config.Configurable
import
scala.collection.JavaConversions._
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
View file @
9812237c
...
...
@@ -38,7 +38,7 @@ trait ToolCommand extends MainCommand with Logging {
}
}
text
"Log level"
validate
{
case
"debug"
|
"info"
|
"warn"
|
"error"
=>
success
case
_
=>
failure
(
"Log level must be <debug/info/warn/error>"
)
case
_
=>
failure
(
"Log level must be <debug/info/warn/error>"
)
}
opt
[
Unit
](
'h'
,
"help"
)
foreach
{
_
=>
System
.
err
.
println
(
this
.
usage
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
View file @
9812237c
...
...
@@ -15,7 +15,8 @@
*/
package
nl.lumc.sasc.biopet.core.config
import
java.io.
{
PrintWriter
,
File
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.Logging
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.ConfigUtils._
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
View file @
9812237c
...
...
@@ -16,6 +16,7 @@
package
nl.lumc.sasc.biopet.core.config
import
java.io.File
import
nl.lumc.sasc.biopet.utils.ConfigUtils._
class
ConfigValue
(
val
requestIndex
:
ConfigValueIndex
,
val
foundIndex
:
ConfigValueIndex
,
val
value
:
Any
,
val
default
:
Boolean
)
{