Commit 8ba7938f authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
Browse files

Merge branch 'develop' into revert-69-fix-BIOPET-654

parents 0211653b 1f2295c2
...@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference { ...@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var R2: File = _ var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R") @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") @Output(doc = "Output file SAM", shortName = "output")
var output: File = _ var output: File = _
...@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference { ...@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var k: Option[Int] = config("k") var k: Option[Int] = config("k")
var r: Option[Float] = config("r") var r: Option[Float] = config("r")
var S: Boolean = config("S", default = false) 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 w: Option[Int] = config("w")
var d: Option[Int] = config("d") var d: Option[Int] = config("d")
var c: Option[Int] = config("c") var c: Option[Int] = config("c")
...@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference { ...@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
if (reference == null) reference = referenceFasta() if (reference == null) reference = referenceFasta()
} }
def cmdLine = { def cmdLine: String = {
required(executable) + required(executable) +
required("mem") + required("mem") +
optional("-k", k) + optional("-k", k) +
......
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