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76da8883

Commit 76da8883 authored 9 years ago by Sander van der Zeeuw

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added proper piping to bcftools and mpileup. [GENTRAP VARSCAN SHOULD BE TESTED]

parent 695ef882

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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala 47 additions, 9 deletions

...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala 4 additions, 7 deletions

...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala 9 additions, 20 deletions

...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala 2 additions, 2 deletions

...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala 15 additions, 27 deletions

...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

with 77 additions and 65 deletions

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