Commit d1b4060c authored 9 years ago by Sander Bollen

Merge branch 'feature-split_modules' into 'develop'

Feature split modules

Fix for #197 and #203 

See merge request !235

parents b7ae99c2 baf41943

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protected/biopet-gatk-extensions/pom.xml 1 addition, 1 deletion

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 1 addition, 1 deletion

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

.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala 1 addition, 1 deletion

...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

with 20 additions and 20 deletions

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