Commit ede612ee authored 10 years ago by Peter van 't Hof

Merge branch 'develop' into feature-summary

Conflicts:
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

parents 38194b88 bec375ba

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log4j.properties 25 additions, 0 deletions

log4j.properties
protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala 24 additions, 16 deletions

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protected/basty/src/test/resources/log4j.properties 25 additions, 0 deletions

protected/basty/src/test/resources/log4j.properties
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala 2 additions, 2 deletions

...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.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/HaplotypeCaller.scala 3 additions, 3 deletions

...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala 1 addition, 1 deletion

.../nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala 1 addition, 1 deletion

.../sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala 3 additions, 3 deletions

...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala 4 additions, 4 deletions

...ala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
protected/biopet-gatk-extensions/src/test/resources/log4j.properties 25 additions, 0 deletions

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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala 2 additions, 5 deletions

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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala 6 additions, 7 deletions

...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala 8 additions, 10 deletions

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala 4 additions, 6 deletions

...sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 14 additions, 16 deletions

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
protected/biopet-gatk-pipelines/src/test/resources/log4j.properties 25 additions, 0 deletions

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protected/biopet-protected-package/src/test/resources/log4j.properties 25 additions, 0 deletions

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protected/log4j.properties 25 additions, 0 deletions

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protected/src/src/test/resources/log4j.properties 25 additions, 0 deletions

protected/src/src/test/resources/log4j.properties

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