Commit 806eaa66 authored 9 years ago by Peter van 't Hof

Merge remote-tracking branch 'origin/develop' into feature-fixed_values

Conflicts:
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
	public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala

parents 4e4bfbeb d1b4060c

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docs/tools/SamplesTsvToJson.md 1 addition, 1 deletion

docs/tools/SamplesTsvToJson.md
pom.xml 1 addition, 1 deletion

pom.xml
protected/biopet-gatk-extensions/pom.xml 2 additions, 2 deletions

protected/biopet-gatk-extensions/pom.xml
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala 1 addition, 1 deletion

...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala 1 addition, 1 deletion

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala 1 addition, 1 deletion

.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala 1 addition, 1 deletion

...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala 1 addition, 1 deletion

...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala 1 addition, 1 deletion

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

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

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

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

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

...mc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala 1 addition, 1 deletion

.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala 1 addition, 1 deletion

.../sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala 1 addition, 1 deletion

.../lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala 1 addition, 1 deletion

...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
protected/biopet-gatk-pipelines/pom.xml 2 additions, 2 deletions

protected/biopet-gatk-pipelines/pom.xml
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala 1 addition, 1 deletion

...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala

with 22 additions and 22 deletions

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