Commit 8b7765a4 authored 9 years ago by Peter van 't Hof

Switched to reference module

parent b2fd3e7c

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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala 5 additions, 1 deletion

.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala 8 additions, 3 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala 2 additions, 2 deletions

...src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala 4 additions, 3 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala 7 additions, 4 deletions

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala 8 additions, 2 deletions

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala 6 additions, 1 deletion

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala 8 additions, 2 deletions

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala 8 additions, 2 deletions

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala 6 additions, 1 deletion

...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala 6 additions, 3 deletions

.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala 8 additions, 2 deletions

...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala 7 additions, 1 deletion

...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala 4 additions, 14 deletions

...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala 0 additions, 2 deletions

...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala 2 additions, 20 deletions

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala 6 additions, 3 deletions

...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

with 95 additions and 66 deletions

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