From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 23 Nov 2017 12:51:15 +0000 (+0000)
Subject: JAL-2808 removed field filters; sort CSQ data by key
X-Git-Tag: Release_2_11_0~106
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a0b04a3977a19395cf95f3535a9fc6b04c754a3a;p=jalview.git

JAL-2808 removed field filters; sort CSQ data by key
---

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)
     {