From 510ee91e928bcee73eb68f449eb7c2e059821664 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Mon, 4 Dec 2023 11:31:13 +0100
Subject: [PATCH] Fix error in total variants calculation

---
 .../java/genepi/riskscore/commands/CreateCollectionCommand.java  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/genepi/riskscore/commands/CreateCollectionCommand.java b/src/main/java/genepi/riskscore/commands/CreateCollectionCommand.java
index c8ed5db..6487e27 100644
--- a/src/main/java/genepi/riskscore/commands/CreateCollectionCommand.java
+++ b/src/main/java/genepi/riskscore/commands/CreateCollectionCommand.java
@@ -105,6 +105,7 @@ public Integer call() throws Exception {
                             nextVariant = readVariant(readers[i], format);
                             read = false;
                         }catch (VariantReadingException e){
+                            totalVariants[i]++;
                             ignoredVariants[i]++;
                         } catch (Exception e) {
                             throw new RuntimeException("File " + filenames[i], e);