Commit d6a28af2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Code style fix

parent 448cb3dd
......@@ -13,10 +13,9 @@ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard._
import org.broadinstitute.sting.queue.function._
import scala.util.parsing.json._
import org.broadinstitute.sting.utils.variant._
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType
class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
qscript =>
def this() = this(null)
@Argument(doc="Only Sample",shortName="sample", required=false)
......@@ -111,7 +110,7 @@ class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
}
realignerTargetCreator.isIntermediate = true
add(realignerTargetCreator)
val indelRealigner = new IndelRealigner with gatkArguments {
this.I :+= inputBam
this.targetIntervals = realignerTargetCreator.o
......@@ -163,7 +162,7 @@ class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
if (configContains("scattercount", "haplotypecaller")) this.scatterCount = config("scattercount", 1, "haplotypecaller")
this.input_file = bamfiles
this.out = outputfile
if (dbsnp != null) this.dbsnp = qscript.dbsnp
if (configContains("dbsnp")) this.dbsnp = config("dbsnp")
this.nct = 3
this.memoryLimit = this.nct * 2
......
Supports Markdown
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