Commit 34b35a99 authored by Peter van 't Hof's avatar Peter van 't Hof

added exextion on from region

parent 97803088
......@@ -63,7 +63,9 @@ object ExtractAlignedFastq extends ToolCommand {
def intFromCoord(s: String): Int = s.replaceAll(",", "").replaceAll("\\.", "").toInt
inStrings.map {
case ptn1(chr, start, end) if intFromCoord(end) > intFromCoord(start) => new Interval(chr, intFromCoord(start), intFromCoord(end))
case ptn1(chr, start, end) if intFromCoord(end) >= intFromCoord(start) => new Interval(chr, intFromCoord(start), intFromCoord(end))
case ptn1(chr, start, end) if intFromCoord(end) < intFromCoord(start) =>
throw new IllegalStateException(s"end is higher then start: $chr:$start-$end")
case ptn2(chr, start) =>
val startCoord = intFromCoord(start)
new Interval(chr, startCoord, startCoord)
......
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