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Commit fbba2eb3 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix compile error

parent 05bf28b2
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......@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{File, PrintWriter}
import java.io.{ File, PrintWriter }
import cern.jet.random.Binomial
import cern.jet.random.engine.RandomEngine
......@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.mutable
import scala.collection.mutable.ArrayBuffer
import scala.io.Source
import scala.math.{floor, round}
import scala.math.{ floor, round }
object MpileupToVcf extends ToolCommand {
case class Args(input: File = null, output: File = null, sample: String = null, minDP: Int = 8, minAP: Int = 2,
......@@ -76,7 +76,7 @@ object MpileupToVcf extends ToolCommand {
writer.println("##FORMAT=<ID=RRC,Number=1,Type=Integer,Description=\"Reference Reverse Reads\">")
writer.println("##FORMAT=<ID=AFC,Number=A,Type=Integer,Description=\"Alternetive Forward Reads\">")
writer.println("##FORMAT=<ID=ARC,Number=A,Type=Integer,Description=\"Alternetive Reverse Reads\">")
writer.println(s"##FORMAT=<ID=SEQ-ERR,Number=R,Type=Float,Description=\"Probilty to not be a sequence error with error rate ${commandArgs.seqError}\">")
writer.println("##FORMAT=<ID=SEQ-ERR,Number=R,Type=Float,Description=\"Probilty to not be a sequence error with error rate " + commandArgs.seqError + "\">")
writer.println("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">")
writer.println("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" + commandArgs.sample)
val inputStream = if (commandArgs.input != null) {
......
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