Commit fb25247e authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing nullpointer

parent a76b4665
...@@ -97,6 +97,7 @@ class ShivaVariantcalling(val parent: Configurable) extends QScript ...@@ -97,6 +97,7 @@ class ShivaVariantcalling(val parent: Configurable) extends QScript
cv.rod_priority_list = Some(callers.filter(_.mergeVcfResults).map(_.name).mkString(",")) cv.rod_priority_list = Some(callers.filter(_.mergeVcfResults).map(_.name).mkString(","))
for (caller <- callers) { for (caller <- callers) {
caller.inputBams = inputBams caller.inputBams = inputBams
caller.inputBqsrFiles = inputBqsrFiles
caller.namePrefix = namePrefix caller.namePrefix = namePrefix
caller.outputDir = new File(outputDir, caller.name) caller.outputDir = new File(outputDir, caller.name)
add(caller) add(caller)
......
...@@ -33,7 +33,7 @@ trait Variantcaller extends QScript with BiopetQScript with Reference { ...@@ -33,7 +33,7 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
* Map of samplename -> (preprocessed) bam file * Map of samplename -> (preprocessed) bam file
*/ */
var inputBams: Map[String, File] = _ var inputBams: Map[String, File] = _
var inputBqsrFiles: Map[String, File] = _ var inputBqsrFiles: Map[String, File] = Map()
def init() = {} def init() = {}
......
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