From ce20a3c6f8fd039db3897bcdc1da8323a798d517 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Wed, 31 Jul 2019 17:15:54 +0200
Subject: [PATCH] Check for FWD/REV swap

---
 src/main/java/genepi/mut/objects/VariantLine.java | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/main/java/genepi/mut/objects/VariantLine.java b/src/main/java/genepi/mut/objects/VariantLine.java
index 8d016fe..b9861fa 100644
--- a/src/main/java/genepi/mut/objects/VariantLine.java
+++ b/src/main/java/genepi/mut/objects/VariantLine.java
@@ -398,9 +398,8 @@ public String toRawString() {
 
 	}
 
-	// TODO check topFWD == minorREV && topREV == minorFWD
 	private boolean checkBases(char topFWD, char topREV, char minorFWD, char minorREV) {
-		return (minorFWD == minorREV && topFWD == topREV);
+		return (minorFWD == minorREV && topFWD == topREV ) || (topFWD == minorREV && topREV == minorFWD && topBasePercentsFWD >= 0.4 && topBasePercentsFWD <= 0.6);
 	}
 
 	private char detectMinorFWD(double minorPercentage) {