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e972a0d1

Commit e972a0d1 authored 9 years ago by Peter van 't Hof

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Merge branch 'fix-278' into 'develop'

Added fix mpileup for bcftools

fixes #278 

See merge request !326

parents 0b8f1ada fdfcf218

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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala 1 addition, 1 deletion

...sc/biopet/core/extensions/PythonCommandLineFunction.scala
public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py 34 additions, 0 deletions

...lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py
public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py 3 additions, 2 deletions

...ces/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala 12 additions, 0 deletions

.../nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala 2 additions, 0 deletions

...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala 3 additions, 2 deletions

...sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/BcftoolsSingleSample.scala 3 additions, 4 deletions

...pipelines/shiva/variantcallers/BcftoolsSingleSample.scala

with 58 additions and 9 deletions

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