JAL-2808 JAL-2850 update spike build to latest

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 9addfaa..de2f18a 100644 (file)
--- 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<?>))
     {