Remove val in for loops

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala

@@ -79,10 +79,10 @@ object BedToInterval extends ToolCommand {
     val bedFile = Source.fromFile(commandArgs.inputFile)
     for (
       line <- bedFile.getLines;
-      val split = line.split("\t") if split.size >= 3;
-      val chr = split(0);
-      val start = split(1);
-      val stop = split(2) if start forall Character.isDigit if stop forall Character.isDigit
+      split = line.split("\t") if split.size >= 3;
+      chr = split(0);
+      start = split(1);
+      stop = split(2) if start forall Character.isDigit if stop forall Character.isDigit
     ) {
       if (!refsMap.contains(chr)) throw new IllegalStateException("Chr '" + chr + "' in bed file not found in bam file")
       writer.write(chr + "\t" + start + "\t" + stop + "\t")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala

@@ -37,7 +37,7 @@ object FindRepeatsPacBio extends ToolCommand {
 
     for (
       bedLine <- Source.fromFile(commandArgs.inputBed).getLines;
-      val values = bedLine.split("\t"); if values.size >= 3
+      values = bedLine.split("\t"); if values.size >= 3
     ) {
       val interval = new QueryInterval(bamHeader.getSequenceIndex(values(0)), values(1).toInt, values(2).toInt)
       val bamIter = bamReader.query(Array(interval), false)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

@@ -115,7 +115,7 @@ object MpileupToVcf extends ToolCommand {
     class Counts(var forward: Int, var reverse: Int)
     for (
       line <- inputStream;
-      val values = line.split("\t");
+      values = line.split("\t");
       if values.size > 5
     ) {
       val chr = values(0)