From a303b81242b1e3e7c1fdd530806d9a6e69f743a5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 29 May 2019 16:17:10 +0100
Subject: [PATCH] JAL-2738 error logging if no ##reference found

---
 src/jalview/io/vcf/VCFLoader.java |    2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 04c73b5..622da73 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -382,6 +382,8 @@ public class VCFLoader
   {
     if (reference == null)
     {
+      Cache.log.error("No VCF ##reference found, defaulting to "
+              + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
       reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
     }
     reference = reference.toLowerCase();
-- 
1.7.10.2