JAL-3375 ignore '.' values for VCF data

[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 7bf7791..053b52f 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -51,6 +51,8 @@ import htsjdk.variant.vcf.VCFInfoHeaderLine;
  */
 public class VCFLoader
 {
+  private static final String NO_VALUE = ".";
+
   private static final String DEFAULT_SPECIES = "homo_sapiens";
 
   /**
@@ -877,7 +879,7 @@ public class VCFLoader
 
     if (att instanceof String)
     {
-      return (String) att;
+      return NO_VALUE.equals(att) ? null : (String) att;
     }
     else if (att instanceof ArrayList)
     {