Commit 98dfb61f authored 10 years ago by Wai Yi Leung

Merging develop into branch and fix Mapping.scala and Flexiprep.scala (merging conflicts and typos)

parents 700ced12 8be170d4

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protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala 1 addition, 1 deletion

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala 1 addition, 1 deletion

...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala 2 additions, 2 deletions

...ala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala 29 additions, 29 deletions

...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala 1 addition, 2 deletions

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 8 additions, 5 deletions

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala 0 additions, 87 deletions

...umc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/SampleCompareMetrics.scala 0 additions, 153 deletions

...umc/sasc/biopet/pipelines/gatk/SampleCompareMetrics.scala
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala 0 additions, 1 deletion

.../nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gatk/plotHeatmap.R 0 additions, 24 deletions

...esources/nl/lumc/sasc/biopet/pipelines/gatk/plotHeatmap.R
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R 35 additions, 0 deletions

...rc/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotXY.R 20 additions, 0 deletions

...ork/src/main/resources/nl/lumc/sasc/biopet/tools/plotXY.R
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 6 additions, 8 deletions

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 2 additions, 2 deletions

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala 2 additions, 2 deletions

...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala 8 additions, 8 deletions

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala 2 additions, 2 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala 6 additions, 6 deletions

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala 14 additions, 0 deletions

...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala

with 138 additions and 334 deletions

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