From a4c2ece43ff148812e3dacbcc946eed43b4dd09e Mon Sep 17 00:00:00 2001
From: JudithNeukamm <judith.neukamm@uzh.ch>
Date: Mon, 8 Jun 2020 17:00:11 +0200
Subject: [PATCH] Bug fix for 'N' instead of reference call.

---
 src/main/java/MultiVCFAnalyzer.java | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/main/java/MultiVCFAnalyzer.java b/src/main/java/MultiVCFAnalyzer.java
index 0beb9f1..cbb9876 100644
--- a/src/main/java/MultiVCFAnalyzer.java
+++ b/src/main/java/MultiVCFAnalyzer.java
@@ -307,7 +307,11 @@ public static void main(String[] args) throws Exception
 				else if(allelCols[0].equals("0/0"))
 				{
 					qual = Double.parseDouble(cols[5]);
-					cov=Integer.parseInt(allelCols[1]);
+					if(allelCols.length==3){
+						cov=Integer.parseInt(allelCols[2]);
+					} else {
+						cov=Integer.parseInt(allelCols[1]);
+					}
 					covCount+=cov;
 					
 					if(qual>=minQual && cov >= minCov)