From b402d8988a33e8cde50026531f44e2442ec2d8b1 Mon Sep 17 00:00:00 2001
From: Alex Leonard <alexander.leonard@usys.ethz.ch>
Date: Fri, 11 Nov 2022 09:38:35 +0100
Subject: [PATCH] Correctly parseInt the SUPP entry, not the string itself.

---
 src/VariantOutput.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/VariantOutput.java b/src/VariantOutput.java
index f364627..c875f68 100644
--- a/src/VariantOutput.java
+++ b/src/VariantOutput.java
@@ -404,7 +404,7 @@ void updateOutputVariant(int sample, VcfEntry entry, int groupNumber) throws Exc
 				}
 				else if(entry.hasInfoField("SUPP"))
 				{
-					varCallsCount = Integer.parseInt("SUPP");
+					varCallsCount = Integer.parseInt(entry.getInfo("SUPP"));
 				}
 				consensus[groupNumber].setInfo("VARCALLS", 
 						varCallsCount + Integer.parseInt(consensus[groupNumber].getInfo("VARCALLS")) + "");