Commit 53da62be authored by Sander Bollen's avatar Sander Bollen
Browse files

fix some more

parent 3ce114fa
...@@ -11,6 +11,6 @@ abstract class Xhmm extends BiopetCommandLineFunction with Version { ...@@ -11,6 +11,6 @@ abstract class Xhmm extends BiopetCommandLineFunction with Version {
executable = config("exe", namespace = "xhmm", default = "xhmm") executable = config("exe", namespace = "xhmm", default = "xhmm")
def versionCommand = executable + required("--version") def versionCommand = executable + " --version"
def versionRegex = """xhmm (.*)""".r def versionRegex = """xhmm (.*)""".r
} }
...@@ -94,6 +94,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { ...@@ -94,6 +94,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
val genotype = new XhmmGenotype(this) val genotype = new XhmmGenotype(this)
genotype.inputXcnv = discover.outputXcnv genotype.inputXcnv = discover.outputXcnv
genotype.inputMatrix = secondMatrix.outputMatrix genotype.inputMatrix = secondMatrix.outputMatrix
genotype.r = thirdMatrix.outputMatrix
genotype.outputVcf = new File(xhmmDir, "xhmm.vcf") genotype.outputVcf = new File(xhmmDir, "xhmm.vcf")
add(genotype) add(genotype)
......
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