Check for FWD/REV swap

seppinho · Jul 31, 2019 · ce20a3c · ce20a3c
1 parent 157da51
commit ce20a3c
Showing 1 changed file with 1 addition and 2 deletions.
diff --git 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) {