Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
a81bce67
Commit
a81bce67
authored
Sep 10, 2015
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Moved config to utils
parent
10e09e28
Changes
189
Expand all
Hide whitespace changes
Inline
Side-by-side
Showing
189 changed files
with
218 additions
and
220 deletions
+218
-220
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
+1
-1
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
-1
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
-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
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
+1
-1
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
-1
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
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
...biopet/extensions/gatk/broad/RealignerTargetCreator.scala
+1
-1
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
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
.../sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
+1
-1
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
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
+1
-1
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
+1
-1
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
+1
-1
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+1
-1
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+1
-1
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
...sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
+1
-1
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+1
-1
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/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
...lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.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
+1
-1
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+1
-1
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+1
-1
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+1
-1
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+1
-1
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+1
-1
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+1
-1
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+1
-26
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+1
-1
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
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
...ain/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.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
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+1
-1
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
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+1
-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
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+1
-1
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/Tabix.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+1
-1
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
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
...lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
+1
-1
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
-1
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/clever/CleverCaller.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
+1
-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/ConiferExport.scala
...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.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
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
+1
-1
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/igvtools/IGVToolsCount.scala
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
+1
-1
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
+1
-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
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+1
-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
+1
-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
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
.../scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
...ala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
.../nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
+1
-1
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
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
.../nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
+1
-1
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
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
...ain/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
...main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
...main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
...rk/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
...est/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
...t/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
...la/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
+1
-1
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
...a/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
+1
-1
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+2
-4
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
...ls/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
+25
-0
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
.../main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
+3
-3
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala
.../scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala
+1
-1
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueIndex.scala
...a/nl/lumc/sasc/biopet/utils/config/ConfigValueIndex.scala
+1
-1
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
...scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
+3
-3
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+1
-1
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
...scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
+1
-1
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+1
-1
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+1
-1
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
...cala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+1
-1
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+1
-1
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+1
-1
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
...la/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+1
-1
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+1
-1
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/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
...nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala
...c/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
.../biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
...sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala
...mc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
...t/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
...c/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
.../lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
+1
-1
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+1
-1
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
...l/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
+1
-1
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
...nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
+1
-1
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.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
+1
-1
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+1
-1
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
.../biopet/pipelines/mapping/scripts/TophatRecondition.scala
+1
-1
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+1
-1
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+1
-1
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
+1
-1
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+1
-1
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+1
-1
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+1
-1
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+1
-1
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+1
-1
public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+1
-1
No files found.
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.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 @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
ApplyRecalibration
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
ApplyRecalibration
with
GatkGeneral
{
scatterCount
=
config
(
"scattercount"
,
default
=
0
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
BaseRecalibrator
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
,
default
=
1
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
CombineGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineGVCFs
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
CombineVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineVariants
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
GenotypeGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
GenotypeGVCFs
with
GatkGeneral
{
annotation
++=
config
(
"annotation"
,
default
=
Seq
(
"FisherStrand"
,
"QualByDepth"
,
"ChromosomeCounts"
)).
asStringList
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
a81bce67
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class
HaplotypeCaller
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
HaplotypeCaller
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
IndelRealigner
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
IndelRealigner
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
PrintReads
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
PrintReads
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
RealignerTargetCreator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
RealignerTargetCreator
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
SelectVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
SelectVariants
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @
a81bce67
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
UnifiedGenotyper
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
UnifiedGenotyper
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
VariantAnnotator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantAnnotator
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
VariantEval
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantEval
with
GatkGeneral
{
override
def
beforeGraph
()
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
class
VariantRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantRecalibrator
with
GatkGeneral
{
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
View file @
a81bce67
...
...
@@ -6,7 +6,7 @@
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.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
View file @
a81bce67
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
View file @
a81bce67
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
GenotypeGVCFs
,
SelectVariants
}
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
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.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
CombineGVCFs
,
CombineVariants
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
SamToFastq
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
View file @
a81bce67
...
...
@@ -6,7 +6,7 @@
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.
utils
.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 @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.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._
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
a81bce67
...
...
@@ -6,7 +6,7 @@
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.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
ShivaTrait
,
ShivaVariantcallingTrait
}
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
View file @
a81bce67
...
...
@@ -6,7 +6,7 @@
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.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad.GenotypeGVCFs
import
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
a81bce67
...
...
@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.
core
.config.Config
import
nl.lumc.sasc.biopet.
utils
.config.Config
import
nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
SortSam
}
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
a81bce67
...
...
@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.
core
.config.Config
import
nl.lumc.sasc.biopet.
utils
.config.Config
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
...
...
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.WigToBigWig
import
nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
...
...
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.queue.function.InProcessFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.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
}
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportBuilder
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summary
,
SummaryValue
}
import
nl.lumc.sasc.biopet.extensions.rscript.
{
StackedBarPlot
,
LinePlot
}
...
...
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.
core
.config.Config
import
nl.lumc.sasc.biopet.
utils
.config.Config
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
...
...
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
a81bce67
...
...
@@ -16,7 +16,7 @@
package
nl.lumc.sasc.biopet.pipelines.basty
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
FileInputStream
}
import
java.security.MessageDigest
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.queue.function.CommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.Input
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.queue.QSettings
...
...
@@ -103,28 +103,3 @@ trait BiopetQScript extends Configurable with GatkLogging {
add
(
function
)
}
}
object
BiopetQScript
extends
Logging
{
private
val
errors
:
ListBuffer
[
Exception
]
=
ListBuffer
()
def
addError
(
error
:
String
,
debug
:
String
=
null
)
:
Unit
=
{
val
msg
=
error
+
(
if
(
debug
!=
null
&&
logger
.
isDebugEnabled
)
"; "
+
debug
else
""
)
errors
.
append
(
new
Exception
(
msg
))
}
protected
def
checkErrors
()
:
Unit
=
{
if
(
errors
.
nonEmpty
)
{
logger
.
error
(
"*************************"
)
logger
.
error
(
"Biopet found some errors:"
)
if
(
logger
.
isDebugEnabled
)
{
for
(
e
<-
errors
)
{
logger
.
error
(
e
.
getMessage
)
logger
.
debug
(
e
.
getStackTrace
.
mkString
(
"Stack trace:\n"
,
"\n"
,
"\n"
))
}
}
else
{
errors
.
map
(
_
.
getMessage
).
sorted
.
distinct
.
foreach
(
logger
.
error
(
_
))
}
throw
new
IllegalStateException
(
"Biopet found errors"
)
}
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.
core
.config.Config
import
nl.lumc.sasc.biopet.
utils
.config.Config
import
nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
import
nl.lumc.sasc.biopet.utils.Logging
import
org.apache.log4j.
{
PatternLayout
,
WriterAppender
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
htsjdk.samtools.reference.IndexedFastaSequenceFile
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
scala.collection.JavaConversions._
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
View file @
a81bce67
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Argument
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core.summary
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
BiopetCommandLineFunctionTrait
,
BiopetJavaCommandLineFunction
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.
{
LastCommitHash
,
Version
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/** Wrapper for the bgzip command */
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
View file @
a81bce67
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
View file @
a81bce67
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configu