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Commit 9c66f418 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
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Merge branch 'develop' into fix-BIOPET-368

parents 077a520a 1f2295c2
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @ 9c66f418
......@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
var reference: File = null
var reference: File = _
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
......@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var k: Option[Int] = config("k")
var r: Option[Float] = config("r")
var S: Boolean = config("S", default = false)
var M: Boolean = config("M", default = true)
var M: Boolean = config("M", default = false)
var w: Option[Int] = config("w")
var d: Option[Int] = config("d")
var c: Option[Int] = config("c")
......@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
if (reference == null) reference = referenceFasta()
}
def cmdLine = {
def cmdLine: String = {
required(executable) +
required("mem") +
optional("-k", k) +
......
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