Commit 9812237c authored 9 years ago by Peter van 't Hof

Optimize imports

parent 7f2580f2

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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala 1 addition, 0 deletions

...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, 0 deletions

...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, 0 deletions

.../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, 0 deletions

...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, 0 deletions

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

.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala 1 addition, 0 deletions

...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala 1 addition, 0 deletions

...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, 0 deletions

...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, 0 deletions

...biopet/extensions/gatk/broad/RealignerTargetCreator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala 1 addition, 0 deletions

...mc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala 1 addition, 0 deletions

.../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, 0 deletions

.../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, 0 deletions

...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala 2 additions, 2 deletions

.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala 2 additions, 3 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 7 additions, 9 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 1 addition, 2 deletions

...sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 5 additions, 4 deletions

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

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

with 32 additions and 22 deletions

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