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622b7500

Commit 622b7500 authored 8 years ago by Peter van 't Hof

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Convert more to biopet values

parent e57304d0

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Changes 6

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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala 4 additions, 4 deletions

...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala 11 additions, 59 deletions

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala 14 additions, 27 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 21 additions, 29 deletions

...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala 22 additions, 66 deletions

...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala 4 additions, 1 deletion

...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

with 76 additions and 186 deletions

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