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24aa443b

Commit 24aa443b authored 9 years ago by Wai Yi Leung

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Merge branch 'fix-small_fixes' into 'develop'

Fix small fixes

Fixes #299 and #300 

See merge request !353

parents 259dd8e7 1bd1056d

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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 12 additions, 5 deletions

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala 2 additions, 2 deletions

.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala 2 additions, 2 deletions

.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala 150 additions, 2 deletions

...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala 3 additions, 0 deletions

.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala 1 addition, 1 deletion

.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala 2 additions, 2 deletions

...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala 2 additions, 9 deletions

...asc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala 11 additions, 8 deletions

...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

with 185 additions and 31 deletions

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