diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala index 48d658358ae9964a5fce214d82d7c6850bca78d0..cde91a20e19bda9cdfe8e97a573b6ea3467af78f 100644 --- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala +++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala @@ -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) {