From 34b35a99fd3145e79ad86aabaef06e28a5123bab Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Wed, 24 Aug 2016 11:39:34 +0200 Subject: [PATCH] added exextion on from region --- .../scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala index 6d655c5ea..05c274925 100644 --- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala +++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala @@ -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) -- GitLab