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3a0b6423

Commit 3a0b6423 authored 10 years ago by bow

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Merge branch 'feature-toolcommands' into 'develop'

Feature toolcommands

Added 4 tools from Sage
see also #67

See merge request !19

parents 063c377b 6f44aea3

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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala 6 additions, 2 deletions

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala 7 additions, 3 deletions

.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala 8 additions, 6 deletions

.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala 17 additions, 15 deletions

.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala 22 additions, 20 deletions

...main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala 44 additions, 37 deletions

...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala 35 additions, 33 deletions

...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala

with 139 additions and 116 deletions

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