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9c5c1703

Commit 9c5c1703 authored 9 years ago by Sander Bollen

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Merge branch 'fix-coverage_piping' into 'develop'

Fix coverage piping

Fixes #230 

still need testing

See merge request !257

parents 4258ac1b 99a3ba0a

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public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 10 additions, 19 deletions

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala 5 additions, 6 deletions

...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala 1 addition, 6 deletions

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala 5 additions, 11 deletions

...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala 4 additions, 0 deletions

...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala 6 additions, 3 deletions

.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala 1 addition, 1 deletion

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

with 32 additions and 46 deletions

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