Commit 5ce11257 authored by Sander Bollen's avatar Sander Bollen

tinyfix

parent b872d91a
...@@ -83,6 +83,7 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with ...@@ -83,6 +83,7 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
* Get set of sample names constituting reference samples for a given sample name * Get set of sample names constituting reference samples for a given sample name
* *
* Reference samples must match the own gender, while excluding own parents (if any) and self * Reference samples must match the own gender, while excluding own parents (if any) and self
*
* @param sampleName: The sample name to create reference set for * @param sampleName: The sample name to create reference set for
* @return * @return
*/ */
...@@ -115,10 +116,7 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with ...@@ -115,10 +116,7 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
def createWisecondorReferenceJobs(referenceSamples: Set[Sample], outputDirectory: File): List[QFunction] = { def createWisecondorReferenceJobs(referenceSamples: Set[Sample], outputDirectory: File): List[QFunction] = {
val gccs = referenceSamples.map { x => val gccs = referenceSamples.map { x =>
val gcc = new WisecondorGcCorrect(this) val gcc = new WisecondorGcCorrect(this)
x.outputWisecondorCountFile match { x.outputWisecondorCountFile foreach { file => gcc.inputBed = file }
case \/-(file) => gcc.inputBed = file
case _ =>
}
gcc.output = new File(outputDirectory, s"${x.sampleId}.gcc") gcc.output = new File(outputDirectory, s"${x.sampleId}.gcc")
gcc gcc
} }
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment