From f0cccdd0703301fd062d467d63f86b6bd5d956ab Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 4 Aug 2016 14:27:30 +0200
Subject: [PATCH] Build in check for passing correct interval to the tool.
---
.../scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala | 2 +-
1 file changed, 1 insertion(+), 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 13622ef41..6d655c5ea 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 +63,7 @@ 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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