X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvcf%2FVCFLoader.java;fp=src%2Fjalview%2Fio%2Fvcf%2FVCFLoader.java;h=155e7738b67ce6527b9818434e041582b41e2148;hp=2847bd796157aa3ff9d207ced225c6a2f3c2ea43;hb=a0b04a3977a19395cf95f3535a9fc6b04c754a3a;hpb=3013ab968530be65871281fc548c5ffa92a7b7b0

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 2847bd7..155e773 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -27,6 +27,8 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.SortedMap;
+import java.util.TreeMap;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
@@ -55,7 +57,7 @@ public class VCFLoader
 
   private static final String VCF_FIELDS_PREF = "VCF_FIELDS";
 
-  private static final String DEFAULT_VCF_FIELDS = "AF,AC*";
+  private static final String DEFAULT_VCF_FIELDS = ".*";
 
   private static final String DEFAULT_VEP_FIELDS = ".*";// "Allele,Consequence,IMPACT,SWISSPROT,SIFT,PolyPhen,CLIN_SIG";
 
@@ -915,7 +917,8 @@ public class VCFLoader
      * inspect CSQ consequences; where possible restrict to the consequence
      * associated with the current transcript (Feature)
      */
-    Map<String, String> csqValues = new HashMap<>();
+    SortedMap<String, String> csqValues = new TreeMap<>(
+            String.CASE_INSENSITIVE_ORDER);
 
     for (String consequence : consequences)
     {