From fbba2eb33e5121d5b1707c13dda18de115b19f98 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 30 Mar 2016 19:26:54 +0200
Subject: [PATCH] Fix compile error
---
.../main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
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 48d658358..cde91a20e 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) {
--
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