Commit 8e97fe15 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added BamOutput Option to Haplotypecaller

parent feeafebb
......@@ -6,6 +6,7 @@ class ConfigValue(val requestIndex: ConfigValueIndex, val foundIndex: ConfigValu
def getDouble = Configurable.any2double(value)
def getList = Configurable.any2list(value)
def getMap = Configurable.any2map(value)
def getBoolean = Configurable.any2boolean(value)
override def toString: String = {
var output = "key = " + requestIndex.key
......
......@@ -124,7 +124,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
this.input_file = bamfiles
this.out = outputfile
if (configContains("dbsnp")) this.dbsnp = config("dbsnp")
this.nct = config("threads", 3, "haplotypecaller")
this.nct = config("threads", default = 3, submodule = "haplotypecaller")
if (config("outputToBam", default = false, submodule = "haplotypecaller").getBoolean) {
this.bamOutput = outputfile.getAbsolutePath + ".bam"
nct = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
this.memoryLimit = this.nct * 2
// GVCF options
......
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