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biopet.biopet
Commits
55b1b7dd
Commit
55b1b7dd
authored
May 25, 2016
by
Sander Bollen
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change ALL licenses across all files.
parent
556229a0
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517 changed files
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1462 additions
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1013 deletions
+1462
-1013
bam2wig/pom.xml
bam2wig/pom.xml
+1
-2
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+1
-2
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+1
-2
bam2wig/src/test/resources/log4j.properties
bam2wig/src/test/resources/log4j.properties
+1
-2
bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
...sc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
+14
-0
bammetrics/pom.xml
bammetrics/pom.xml
+1
-2
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py
...biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py
+1
-2
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+1
-2
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+1
-2
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
...lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
+1
-2
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
+1
-2
bammetrics/src/test/resources/log4j.properties
bammetrics/src/test/resources/log4j.properties
+1
-2
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+1
-2
basty/pom.xml
basty/pom.xml
+1
-2
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+1
-2
basty/src/test/resources/log4j.properties
basty/src/test/resources/log4j.properties
+1
-2
biopet-aggregate/pom.xml
biopet-aggregate/pom.xml
+16
-0
biopet-core/pom.xml
biopet-core/pom.xml
+1
-2
biopet-core/src/main/resources/log4j.properties
biopet-core/src/main/resources/log4j.properties
+1
-2
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
...c/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
+0
-4
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
...nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
+0
-4
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
...c/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
+1
-2
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
...c/biopet/core/report/ext/css/sortable-theme-bootstrap.css
+1
-2
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js
...s/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js
+0
-15
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/d3.v3.5.5.min.js
...s/nl/lumc/sasc/biopet/core/report/ext/js/d3.v3.5.5.min.js
+0
-15
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js
...rces/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js
+0
-15
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
...es/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
+0
-15
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
...ain/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala
.../nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala
+14
-0
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
.../scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala
...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
...la/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
...a/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
...in/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
...sc/biopet/core/extensions/PythonCommandLineFunction.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
...c/biopet/core/extensions/RscriptCommandLineFunction.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
...mc/sasc/biopet/core/report/MultisampleReportBuilder.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
...in/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
...scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+1
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+1
-2
biopet-core/src/test/resources/log4j.properties
biopet-core/src/test/resources/log4j.properties
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
.../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
...a/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
...ala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
.../scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
...c/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
...scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
...test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
...cala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
+14
-0
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala
...asc/biopet/core/report/MultisampleReportBuilderTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
...a/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala
...a/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
...a/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
...nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
+1
-2
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
+1
-2
biopet-extensions/pom.xml
biopet-extensions/pom.xml
+1
-2
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
...umc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
+1
-2
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py
...lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py
+1
-2
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py
...ces/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
+2
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
.../scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
...ns/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
.../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
.../lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
.../scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
...scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
.../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
...a/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
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-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
...in/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCAssessSignificancePlot.scala
...biopet/extensions/freec/FreeCAssessSignificancePlot.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
...a/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
...a/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
.../lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala
.../lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala
.../lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
...la/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala
...nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ContigScatterFunction.scala
...c/sasc/biopet/extensions/gatk/ContigScatterFunction.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkScatterFunction.scala
...umc/sasc/biopet/extensions/gatk/GatkScatterFunction.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala
...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
...a/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
.../nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/LocusScatterFunction.scala
...mc/sasc/biopet/extensions/gatk/LocusScatterFunction.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
...cala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
.../sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
.../nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
...l/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
...ala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
...umc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
...scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
+1
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+1
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+1
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
+1
-3
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
...in/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
...sc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
...c/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
...c/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
...c/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala
...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
...umc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
.../sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
.../sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
...nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
...asc/biopet/extensions/picard/CollectMultipleMetrics.scala
+1
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
.../biopet/extensions/picard/CollectTargetedPcrMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CreateSequenceDictionary.scala
...c/biopet/extensions/picard/CreateSequenceDictionary.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
...l/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
...ala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
...nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
...a/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
...nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
...scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
...ala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
...mc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
...la/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
...mc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
.../nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
.../lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
...in/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
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-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
...c/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
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biopet-extensions/src/test/resources/log4j.properties
biopet-extensions/src/test/resources/log4j.properties
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
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biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
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biopet-package/pom.xml
biopet-package/pom.xml
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biopet-package/src/test/resources/log4j.properties
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biopet-tools-extensions/pom.xml
biopet-tools-extensions/pom.xml
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
...la/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
...umc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
.../nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
...nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
.../nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
...umc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
...a/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala
...a/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
...la/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
...la/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
...nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
...lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
...mc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
.../scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
...a/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala
.../nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
...scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
...ala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
.../nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
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-2
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
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-2
biopet-tools-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala
.../nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala
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-2
biopet-tools-package/pom.xml
biopet-tools-package/pom.xml
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-2
biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
...ain/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
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-2
biopet-tools/pom.xml
biopet-tools/pom.xml
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-2
biopet-tools/src/main/resources/log4j.properties
biopet-tools/src/main/resources/log4j.properties
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
...main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
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-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
.../scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
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-2
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
.../main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
...in/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
.../main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
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biopet-tools/src/test/resources/README.txt
biopet-tools/src/test/resources/README.txt
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biopet-tools/src/test/resources/log4j.properties
biopet-tools/src/test/resources/log4j.properties
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
.../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
...est/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
.../scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
...rc/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SnptestToVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ValidateFastqTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
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biopet-utils/pom.xml
biopet-utils/pom.xml
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/package.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/LazyCheck.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/MainCommand.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ToolCommand.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueIndex.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/ScatterPlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
...ain/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
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biopet-utils/src/test/resources/log4j.properties
biopet-utils/src/test/resources/log4j.properties
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/BamUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/IoUtilsTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryTest.scala
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biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValueTest.scala
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bump-version.sh
bump-version.sh
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carp/pom.xml
carp/pom.xml
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carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
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carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
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carp/src/test/resources/log4j.properties
carp/src/test/resources/log4j.properties
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carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
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external-example/pom.xml
external-example/pom.xml
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external-example/src/main/scala/org/example/group/ExecutableExample.scala
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external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
...in/scala/org/example/group/pipelines/BiopetPipeline.scala
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external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala
...ain/scala/org/example/group/pipelines/HelloPipeline.scala
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external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
...ala/org/example/group/pipelines/MultisamplePipeline.scala
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external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
...in/scala/org/example/group/pipelines/SimplePipeline.scala
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flexiprep/pom.xml
flexiprep/pom.xml
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/AdapterSequence.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CheckValidateFastq.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
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flexiprep/src/test/resources/fqc_contaminants_v0101.txt
flexiprep/src/test/resources/fqc_contaminants_v0101.txt
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flexiprep/src/test/resources/log4j.properties
flexiprep/src/test/resources/log4j.properties
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
...l/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
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gears/pom.xml
gears/pom.xml
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gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/report/ext/js/gears.js
...l/lumc/sasc/biopet/pipelines/gears/report/ext/js/gears.js
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gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/report/ext/js/krona-2.0.js
...mc/sasc/biopet/pipelines/gears/report/ext/js/krona-2.0.js
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/ExtractUnmappedReads.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
.../lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
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gears/src/test/resources/log4j.properties
gears/src/test/resources/log4j.properties
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKrakenTest.scala
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosedTest.scala
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
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gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
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generate-indexes/pom.xml
generate-indexes/pom.xml
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generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/FastaMerging.scala
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generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
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generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfig.scala
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generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexesTest.scala
...iopet/pipelines/generateindexes/GenerateIndexesTest.scala
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generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfigTest.scala
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gentrap/pom.xml
gentrap/pom.xml
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
.../biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
.../biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
.../sasc/biopet/pipelines/gentrap/measures/Measurement.scala
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gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
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gentrap/src/test/resources/log4j.properties
gentrap/src/test/resources/log4j.properties
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gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
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gwas-test/pom.xml
gwas-test/pom.xml
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gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
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gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala
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gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Spec.scala
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gwas-test/src/test/resources/log4j.properties
gwas-test/src/test/resources/log4j.properties
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gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
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kopisu/pom.xml
kopisu/pom.xml
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
.../sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
...mc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
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kopisu/src/test/resources/log4j.properties
kopisu/src/test/resources/log4j.properties
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kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
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license_header.sh
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log4j.properties
log4j.properties
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mapping/pom.xml
mapping/pom.xml
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mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/scripts/tophat-recondition.py
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+1
-2
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+1
-2
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
...mc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+1
-2
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+1
-2
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
.../biopet/pipelines/mapping/scripts/TophatRecondition.scala
+1
-2
mapping/src/test/resources/log4j.properties
mapping/src/test/resources/log4j.properties
+1
-2
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+1
-2
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
...asc/biopet/pipelines/mapping/MultisampleMappingTest.scala
+14
-0
pom.xml
pom.xml
+3
-2
sage/pom.xml
sage/pom.xml
+1
-2
sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+1
-2
sage/src/test/resources/log4j.properties
sage/src/test/resources/log4j.properties
+1
-2
shiva/pom.xml
shiva/pom.xml
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
...c/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
...lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
...sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
...pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
...asc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCaller.scala
...opet/pipelines/shiva/variantcallers/HaplotypeCaller.scala
+14
-0
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
...ipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
+14
-0
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
.../pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
+14
-0
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
...c/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyper.scala
...pet/pipelines/shiva/variantcallers/UnifiedGenotyper.scala
+14
-0
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
...pelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
+14
-0
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
...biopet/pipelines/shiva/variantcallers/Variantcaller.scala
+1
-2
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
...pelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+1
-2
shiva/src/test/resources/log4j.properties
shiva/src/test/resources/log4j.properties
+1
-2
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
...lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+1
-2
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+1
-2
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+14
-0
src/src/test/resources/log4j.properties
src/src/test/resources/log4j.properties
+1
-2
templates/public_license.txt
templates/public_license.txt
+0
-28
tinycap/pom.xml
tinycap/pom.xml
+1
-2
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
...scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
+1
-2
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala
...nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala
+1
-2
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/measures/FragmentsPerSmallRna.scala
...pet/pipelines/tinycap/measures/FragmentsPerSmallRna.scala
+1
-2
tinycap/src/test/resources/log4j.properties
tinycap/src/test/resources/log4j.properties
+1
-2
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
+14
-0
toucan/pom.xml
toucan/pom.xml
+1
-2
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala
...opet/pipelines/toucan/ManweActivateAfterAnnotImport.scala
+1
-2
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
.../biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
+1
-2
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+1
-2
toucan/src/test/resources/log4j.properties
toucan/src/test/resources/log4j.properties
+1
-2
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
+14
-0
No files found.
bam2wig/pom.xml
View file @
55b1b7dd
...
...
@@ -10,8 +10,7 @@
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
...
...
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
bam2wig/src/test/resources/log4j.properties
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
...
...
bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
View file @
55b1b7dd
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.File
...
...
bammetrics/pom.xml
View file @
55b1b7dd
...
...
@@ -9,8 +9,7 @@
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py
View file @
55b1b7dd
...
...
@@ -9,8 +9,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
bammetrics/src/test/resources/log4j.properties
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
...
...
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
basty/pom.xml
View file @
55b1b7dd
...
...
@@ -9,8 +9,7 @@
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
...
...
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
basty/src/test/resources/log4j.properties
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
...
...
biopet-aggregate/pom.xml
View file @
55b1b7dd
<?xml version="1.0" encoding="UTF-8"?>
<!--
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
-->
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
...
...
biopet-core/pom.xml
View file @
55b1b7dd
...
...
@@ -10,8 +10,7 @@
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
...
...
biopet-core/src/main/resources/log4j.properties
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
View file @
55b1b7dd
/*!
* Bootstrap v3.3.4 (http://getbootstrap.com)
* Copyright 2011-2015 Twitter, Inc.
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
*/
.btn-danger
,
.btn-default
,
.btn-info
,
.btn-primary
,
.btn-success
,
.btn-warning
{
text-shadow
:
0
-1px
0
rgba
(
0
,
0
,
0
,
.2
);
-webkit-box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.15
),
0
1px
1px
rgba
(
0
,
0
,
0
,
.075
);
box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.15
),
0
1px
1px
rgba
(
0
,
0
,
0
,
.075
)}
.btn-danger.active
,
.btn-danger
:active
,
.btn-default.active
,
.btn-default
:active
,
.btn-info.active
,
.btn-info
:active
,
.btn-primary.active
,
.btn-primary
:active
,
.btn-success.active
,
.btn-success
:active
,
.btn-warning.active
,
.btn-warning
:active
{
-webkit-box-shadow
:
inset
0
3px
5px
rgba
(
0
,
0
,
0
,
.125
);
box-shadow
:
inset
0
3px
5px
rgba
(
0
,
0
,
0
,
.125
)}
.btn-danger
.badge
,
.btn-default
.badge
,
.btn-info
.badge
,
.btn-primary
.badge
,
.btn-success
.badge
,
.btn-warning
.badge
{
text-shadow
:
none
}
.btn.active
,
.btn
:active
{
background-image
:
none
}
.btn-default
{
text-shadow
:
0
1px
0
#fff
;
background-image
:
-webkit-linear-gradient
(
top
,
#fff
0
,
#e0e0e0
100%
);
background-image
:
-o-linear-gradient
(
top
,
#fff
0
,
#e0e0e0
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#fff
),
to
(
#e0e0e0
));
background-image
:
linear-gradient
(
to
bottom
,
#fff
0
,
#e0e0e0
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffffffff'
,
endColorstr
=
'#ffe0e0e0'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
;
border-color
:
#dbdbdb
;
border-color
:
#ccc
}
.btn-default
:focus
,
.btn-default
:hover
{
background-color
:
#e0e0e0
;
background-position
:
0
-15px
}
.btn-default.active
,
.btn-default
:active
{
background-color
:
#e0e0e0
;
border-color
:
#dbdbdb
}
.btn-default.disabled
,
.btn-default
:disabled
,
.btn-default
[
disabled
]
{
background-color
:
#e0e0e0
;
background-image
:
none
}
.btn-primary
{
background-image
:
-webkit-linear-gradient
(
top
,
#337ab7
0
,
#265a88
100%
);
background-image
:
-o-linear-gradient
(
top
,
#337ab7
0
,
#265a88
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#337ab7
),
to
(
#265a88
));
background-image
:
linear-gradient
(
to
bottom
,
#337ab7
0
,
#265a88
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff337ab7'
,
endColorstr
=
'#ff265a88'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
;
border-color
:
#245580
}
.btn-primary
:focus
,
.btn-primary
:hover
{
background-color
:
#265a88
;
background-position
:
0
-15px
}
.btn-primary.active
,
.btn-primary
:active
{
background-color
:
#265a88
;
border-color
:
#245580
}
.btn-primary.disabled
,
.btn-primary
:disabled
,
.btn-primary
[
disabled
]
{
background-color
:
#265a88
;
background-image
:
none
}
.btn-success
{
background-image
:
-webkit-linear-gradient
(
top
,
#5cb85c
0
,
#419641
100%
);
background-image
:
-o-linear-gradient
(
top
,
#5cb85c
0
,
#419641
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#5cb85c
),
to
(
#419641
));
background-image
:
linear-gradient
(
to
bottom
,
#5cb85c
0
,
#419641
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff5cb85c'
,
endColorstr
=
'#ff419641'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
;
border-color
:
#3e8f3e
}
.btn-success
:focus
,
.btn-success
:hover
{
background-color
:
#419641
;
background-position
:
0
-15px
}
.btn-success.active
,
.btn-success
:active
{
background-color
:
#419641
;
border-color
:
#3e8f3e
}
.btn-success.disabled
,
.btn-success
:disabled
,
.btn-success
[
disabled
]
{
background-color
:
#419641
;
background-image
:
none
}
.btn-info
{
background-image
:
-webkit-linear-gradient
(
top
,
#5bc0de
0
,
#2aabd2
100%
);
background-image
:
-o-linear-gradient
(
top
,
#5bc0de
0
,
#2aabd2
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#5bc0de
),
to
(
#2aabd2
));
background-image
:
linear-gradient
(
to
bottom
,
#5bc0de
0
,
#2aabd2
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff5bc0de'
,
endColorstr
=
'#ff2aabd2'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
;
border-color
:
#28a4c9
}
.btn-info
:focus
,
.btn-info
:hover
{
background-color
:
#2aabd2
;
background-position
:
0
-15px
}
.btn-info.active
,
.btn-info
:active
{
background-color
:
#2aabd2
;
border-color
:
#28a4c9
}
.btn-info.disabled
,
.btn-info
:disabled
,
.btn-info
[
disabled
]
{
background-color
:
#2aabd2
;
background-image
:
none
}
.btn-warning
{
background-image
:
-webkit-linear-gradient
(
top
,
#f0ad4e
0
,
#eb9316
100%
);
background-image
:
-o-linear-gradient
(
top
,
#f0ad4e
0
,
#eb9316
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#f0ad4e
),
to
(
#eb9316
));
background-image
:
linear-gradient
(
to
bottom
,
#f0ad4e
0
,
#eb9316
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fff0ad4e'
,
endColorstr
=
'#ffeb9316'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
;
border-color
:
#e38d13
}
.btn-warning
:focus
,
.btn-warning
:hover
{
background-color
:
#eb9316
;
background-position
:
0
-15px
}
.btn-warning.active
,
.btn-warning
:active
{
background-color
:
#eb9316
;
border-color
:
#e38d13
}
.btn-warning.disabled
,
.btn-warning
:disabled
,
.btn-warning
[
disabled
]
{
background-color
:
#eb9316
;
background-image
:
none
}
.btn-danger
{
background-image
:
-webkit-linear-gradient
(
top
,
#d9534f
0
,
#c12e2a
100%
);
background-image
:
-o-linear-gradient
(
top
,
#d9534f
0
,
#c12e2a
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#d9534f
),
to
(
#c12e2a
));
background-image
:
linear-gradient
(
to
bottom
,
#d9534f
0
,
#c12e2a
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffd9534f'
,
endColorstr
=
'#ffc12e2a'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
;
border-color
:
#b92c28
}
.btn-danger
:focus
,
.btn-danger
:hover
{
background-color
:
#c12e2a
;
background-position
:
0
-15px
}
.btn-danger.active
,
.btn-danger
:active
{
background-color
:
#c12e2a
;
border-color
:
#b92c28
}
.btn-danger.disabled
,
.btn-danger
:disabled
,
.btn-danger
[
disabled
]
{
background-color
:
#c12e2a
;
background-image
:
none
}
.img-thumbnail
,
.thumbnail
{
-webkit-box-shadow
:
0
1px
2px
rgba
(
0
,
0
,
0
,
.075
);
box-shadow
:
0
1px
2px
rgba
(
0
,
0
,
0
,
.075
)}
.dropdown-menu
>
li
>
a
:focus
,
.dropdown-menu
>
li
>
a
:hover
{
background-color
:
#e8e8e8
;
background-image
:
-webkit-linear-gradient
(
top
,
#f5f5f5
0
,
#e8e8e8
100%
);
background-image
:
-o-linear-gradient
(
top
,
#f5f5f5
0
,
#e8e8e8
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#f5f5f5
),
to
(
#e8e8e8
));
background-image
:
linear-gradient
(
to
bottom
,
#f5f5f5
0
,
#e8e8e8
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fff5f5f5'
,
endColorstr
=
'#ffe8e8e8'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.dropdown-menu
>
.active
>
a
,
.dropdown-menu
>
.active
>
a
:focus
,
.dropdown-menu
>
.active
>
a
:hover
{
background-color
:
#2e6da4
;
background-image
:
-webkit-linear-gradient
(
top
,
#337ab7
0
,
#2e6da4
100%
);
background-image
:
-o-linear-gradient
(
top
,
#337ab7
0
,
#2e6da4
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#337ab7
),
to
(
#2e6da4
));
background-image
:
linear-gradient
(
to
bottom
,
#337ab7
0
,
#2e6da4
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff337ab7'
,
endColorstr
=
'#ff2e6da4'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.navbar-default
{
background-image
:
-webkit-linear-gradient
(
top
,
#fff
0
,
#f8f8f8
100%
);
background-image
:
-o-linear-gradient
(
top
,
#fff
0
,
#f8f8f8
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#fff
),
to
(
#f8f8f8
));
background-image
:
linear-gradient
(
to
bottom
,
#fff
0
,
#f8f8f8
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffffffff'
,
endColorstr
=
'#fff8f8f8'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
;
border-radius
:
4px
;
-webkit-box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.15
),
0
1px
5px
rgba
(
0
,
0
,
0
,
.075
);
box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.15
),
0
1px
5px
rgba
(
0
,
0
,
0
,
.075
)}
.navbar-default
.navbar-nav
>
.active
>
a
,
.navbar-default
.navbar-nav
>
.open
>
a
{
background-image
:
-webkit-linear-gradient
(
top
,
#dbdbdb
0
,
#e2e2e2
100%
);
background-image
:
-o-linear-gradient
(
top
,
#dbdbdb
0
,
#e2e2e2
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#dbdbdb
),
to
(
#e2e2e2
));
background-image
:
linear-gradient
(
to
bottom
,
#dbdbdb
0
,
#e2e2e2
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffdbdbdb'
,
endColorstr
=
'#ffe2e2e2'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
-webkit-box-shadow
:
inset
0
3px
9px
rgba
(
0
,
0
,
0
,
.075
);
box-shadow
:
inset
0
3px
9px
rgba
(
0
,
0
,
0
,
.075
)}
.navbar-brand
,
.navbar-nav
>
li
>
a
{
text-shadow
:
0
1px
0
rgba
(
255
,
255
,
255
,
.25
)}
.navbar-inverse
{
background-image
:
-webkit-linear-gradient
(
top
,
#3c3c3c
0
,
#222
100%
);
background-image
:
-o-linear-gradient
(
top
,
#3c3c3c
0
,
#222
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#3c3c3c
),
to
(
#222
));
background-image
:
linear-gradient
(
to
bottom
,
#3c3c3c
0
,
#222
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff3c3c3c'
,
endColorstr
=
'#ff222222'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
}
.navbar-inverse
.navbar-nav
>
.active
>
a
,
.navbar-inverse
.navbar-nav
>
.open
>
a
{
background-image
:
-webkit-linear-gradient
(
top
,
#080808
0
,
#0f0f0f
100%
);
background-image
:
-o-linear-gradient
(
top
,
#080808
0
,
#0f0f0f
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#080808
),
to
(
#0f0f0f
));
background-image
:
linear-gradient
(
to
bottom
,
#080808
0
,
#0f0f0f
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff080808'
,
endColorstr
=
'#ff0f0f0f'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
-webkit-box-shadow
:
inset
0
3px
9px
rgba
(
0
,
0
,
0
,
.25
);
box-shadow
:
inset
0
3px
9px
rgba
(
0
,
0
,
0
,
.25
)}
.navbar-inverse
.navbar-brand
,
.navbar-inverse
.navbar-nav
>
li
>
a
{
text-shadow
:
0
-1px
0
rgba
(
0
,
0
,
0
,
.25
)}
.navbar-fixed-bottom
,
.navbar-fixed-top
,
.navbar-static-top
{
border-radius
:
0
}
@media
(
max-width
:
767px
){
.navbar
.navbar-nav
.open
.dropdown-menu
>
.active
>
a
,
.navbar
.navbar-nav
.open
.dropdown-menu
>
.active
>
a
:focus
,
.navbar
.navbar-nav
.open
.dropdown-menu
>
.active
>
a
:hover
{
color
:
#fff
;
background-image
:
-webkit-linear-gradient
(
top
,
#337ab7
0
,
#2e6da4
100%
);
background-image
:
-o-linear-gradient
(
top
,
#337ab7
0
,
#2e6da4
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#337ab7
),
to
(
#2e6da4
));
background-image
:
linear-gradient
(
to
bottom
,
#337ab7
0
,
#2e6da4
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff337ab7'
,
endColorstr
=
'#ff2e6da4'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}}
.alert
{
text-shadow
:
0
1px
0
rgba
(
255
,
255
,
255
,
.2
);
-webkit-box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.25
),
0
1px
2px
rgba
(
0
,
0
,
0
,
.05
);
box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.25
),
0
1px
2px
rgba
(
0
,
0
,
0
,
.05
)}
.alert-success
{
background-image
:
-webkit-linear-gradient
(
top
,
#dff0d8
0
,
#c8e5bc
100%
);
background-image
:
-o-linear-gradient
(
top
,
#dff0d8
0
,
#c8e5bc
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#dff0d8
),
to
(
#c8e5bc
));
background-image
:
linear-gradient
(
to
bottom
,
#dff0d8
0
,
#c8e5bc
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffdff0d8'
,
endColorstr
=
'#ffc8e5bc'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
border-color
:
#b2dba1
}
.alert-info
{
background-image
:
-webkit-linear-gradient
(
top
,
#d9edf7
0
,
#b9def0
100%
);
background-image
:
-o-linear-gradient
(
top
,
#d9edf7
0
,
#b9def0
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#d9edf7
),
to
(
#b9def0
));
background-image
:
linear-gradient
(
to
bottom
,
#d9edf7
0
,
#b9def0
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffd9edf7'
,
endColorstr
=
'#ffb9def0'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
border-color
:
#9acfea
}
.alert-warning
{
background-image
:
-webkit-linear-gradient
(
top
,
#fcf8e3
0
,
#f8efc0
100%
);
background-image
:
-o-linear-gradient
(
top
,
#fcf8e3
0
,
#f8efc0
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#fcf8e3
),
to
(
#f8efc0
));
background-image
:
linear-gradient
(
to
bottom
,
#fcf8e3
0
,
#f8efc0
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fffcf8e3'
,
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(
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,
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background-image
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(
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background-image
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,
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,
transparent
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(
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rgba
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border-radius
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4px
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,
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text-shadow
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#286090
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,
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(
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,
left
bottom
,
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(
#337ab7
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top
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0
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to
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0
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100%
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0
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100%
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-o-linear-gradient
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#f2dede
0
,
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100%
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left
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0
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:
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top
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0
,
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100%
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0
,
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100%
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top
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left
bottom
,
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(
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to
(
#f5f5f5
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(
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bottom
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#e8e8e8
0
,
#f5f5f5
100%
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filter
:
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:
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Microsoft
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gradient
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:
repeat-x
;
border-color
:
#dcdcdc
;
-webkit-box-shadow
:
inset
0
1px
3px
rgba
(
0
,
0
,
0
,
.05
),
0
1px
0
rgba
(
255
,
255
,
255
,
.1
);
box-shadow
:
inset
0
1px
3px
rgba
(
0
,
0
,
0
,
.05
),
0
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rgba
(
255
,
255
,
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.1
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\ No newline at end of file
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
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55b1b7dd
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biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
View file @
55b1b7dd
...
...
@@ -8,8 +8,7 @@
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js
View file @
55b1b7dd
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biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/d3.v3.5.5.min.js
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biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js
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biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
View file @
55b1b7dd
/*
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
/*! sortable.js 0.5.0 */
(
function
(){
var
a
,
b
,
c
,
d
,
e
,
f
;
a
=
"
table[data-sortable]
"
,
c
=
/^-
?[
£$¤
]?[\d
,.
]
+%
?
$/
,
f
=
/^
\s
+|
\s
+$/g
,
e
=
"
ontouchstart
"
in
document
.
documentElement
,
b
=
e
?
"
touchstart
"
:
"
click
"
,
d
=
{
init
:
function
(){
var
b
,
c
,
e
,
f
,
g
;
for
(
c
=
document
.
querySelectorAll
(
a
),
g
=
[],
e
=
0
,
f
=
c
.
length
;
f
>
e
;
e
++
)
b
=
c
[
e
],
g
.
push
(
d
.
initTable
(
b
));
return
g
},
initTable
:
function
(
a
){
var
b
,
c
,
e
,
f
,
g
;
if
(
1
===
a
.
tHead
.
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.
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"
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"
)){
for
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"
,
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"
),
e
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),
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=++
f
)
c
=
e
[
b
],
"
false
"
!==
c
.
getAttribute
(
"
data-sortable
"
)
&&
d
.
setupClickableTH
(
a
,
c
,
b
);
return
a
}},
setupClickableTH
:
function
(
a
,
c
,
e
){
var
f
;
return
f
=
d
.
getColumnType
(
a
,
e
),
c
<