X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvcf%2FVCFLoader.java;h=de2f18ad7fa812fefb35350307fff2ed6b1ac322;hb=4073e96c3cb60f28c01cd91ec7f847cafbf01f78;hp=9addfaaa68a6c7861a49e6d919daa95ffa578549;hpb=296593216c47a835f462d1d74a40b41e4818f737;p=jalview.git

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 9addfaa..de2f18a 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -1013,6 +1013,10 @@ public class VCFLoader
   {
     String type = SequenceOntologyI.SEQUENCE_VARIANT;
 
+    /*
+     * could we associate Consequence data with this allele and feature (transcript)?
+     * if so, prefer the consequence term from that data
+     */
     if (csqAlleleFieldIndex == -1) // && snpEffAlleleFieldIndex == -1
     {
       /*
@@ -1021,10 +1025,6 @@ public class VCFLoader
       return type;
     }
 
-    /*
-     * can we associate Consequence data with this allele and feature (transcript)?
-     * if so, prefer the consequence term from that data
-     */
     if (consequence != null)
     {
       String[] csqFields = consequence.split(PIPE_REGEX);
@@ -1190,6 +1190,14 @@ public class VCFLoader
       }
 
       /*
+       * filter out fields we don't want to capture
+       */
+      if (!vcfFieldsOfInterest.contains(key))
+      {
+        continue;
+      }
+
+      /*
        * we extract values for other data which are allele-specific; 
        * these may be per alternate allele (INFO[key].Number = 'A') 
        * or per allele including reference (INFO[key].Number = 'R') 
@@ -1249,7 +1257,6 @@ public class VCFLoader
           String myConsequence)
   {
     Object value = variant.getAttribute(CSQ_FIELD);
-    // TODO if CSQ not present, try ANN (for SnpEff consequence data)?
 
     if (value == null || !(value instanceof List<?>))
     {