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Commit efccec1f authored by Peter van 't Hof's avatar Peter van 't Hof
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Added header to bam file

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public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/ExtractUnmappedReads.scala
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View file @ efccec1f
......@@ -36,6 +36,7 @@ class ExtractUnmappedReads(val root: Configurable) extends QScript with BiopetQS
val samtoolsViewSelectUnmapped = new SamtoolsView(this)
samtoolsViewSelectUnmapped.input = bamFile
samtoolsViewSelectUnmapped.b = true
samtoolsViewSelectUnmapped.h = true
samtoolsViewSelectUnmapped.output = swapExt(outputDir, bamFile, ".bam", "unmapped.bam")
if (paired) samtoolsViewSelectUnmapped.f = List("12")
else samtoolsViewSelectUnmapped.f = List("4")
......
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