Commit c347da53 authored by rhpvorderman's avatar rhpvorderman

Fixed code warnings

parent 1a7d4610
...@@ -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 = _
...@@ -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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