diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala index b05591cbf9af0406659cf331da665a8ab472c28e..0b569d6c40714ffda03ddbd2390342601630d1d3 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala @@ -55,14 +55,13 @@ object ExtractAlignedFastq extends ToolCommand { // by the Interval constructor only accepting ints def intFromCoord(s: String): Int = s.replaceAll(",", "").replaceAll("\\.", "").toInt - inStrings.map(x => x match { + inStrings.map { case ptn1(chr, start, end) => new Interval(chr, intFromCoord(start), intFromCoord(end)) case ptn2(chr, start) => val startCoord = intFromCoord(start) new Interval(chr, startCoord, startCoord) case _ => throw new IllegalArgumentException("Invalid interval string: " + x) - }) - .toIterator + }.toIterator } /**