Commit 0db306c4 authored by Peter van 't Hof's avatar Peter van 't Hof

Merge branch 'fix-extractAlignedFastq' into 'develop'

Build in check for passing correct interval to the tool.

Before this fix it was possible to give a smaller end than start. Fix is tested and works proper.

See merge request !442
parents e5384fc2 13be64ac
......@@ -63,7 +63,7 @@ object ExtractAlignedFastq extends ToolCommand {
def intFromCoord(s: String): Int = s.replaceAll(",", "").replaceAll("\\.", "").toInt
inStrings.map {
case ptn1(chr, start, end) => 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 ptn2(chr, start) =>
val startCoord = intFromCoord(start)
new Interval(chr, startCoord, startCoord)
......
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