Set minimal coverage to 5 (same as in mtDNA-Server)

seppinho · Jan 22, 2019 · 5c0099d · 5c0099d
1 parent c2e5860
commit 5c0099d
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/src/main/java/genepi/mut/util/VariantCaller.java b/src/main/java/genepi/mut/util/VariantCaller.java
@@ -170,12 +170,12 @@ public static double calcLevelTop(VariantLine line) {
 	}
 
 	private static boolean checkAlleleCoverage(VariantLine line, double minorPercentFWD, double minorPercentREV) {
-		if (line.getTopBasePercentsREV() * line.getCovREV() < 3
-				|| (line.getTopBasePercentsFWD() * line.getCovFWD()) < 3) {
+		if (line.getTopBasePercentsREV() * line.getCovREV() <= 5
+				|| (line.getTopBasePercentsFWD() * line.getCovFWD()) <= 5) {
 			return false;
 		}
 
-		if ((minorPercentREV * line.getCovREV() < 3) || (line.getTopBasePercentsFWD() * line.getCovFWD()) < 3) {
+		if ((minorPercentREV * line.getCovREV() <= 5) || (line.getTopBasePercentsFWD() * line.getCovFWD()) <= 5) {
 			return false;
 		}