AF1 filtered - except for non-variant sites

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15825 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/variant/VCFFilter.java

@@ -255,7 +255,8 @@ public class VCFFilter extends JFrame
 
       try
       {
-        if(VCFFilter.MIN_AF1 > 0 && Float.parseFloat(record.getInfoValue("AF1")) < VCFFilter.MIN_AF1)
+        // AF1 filtered - except for non-variant sites
+        if((!record.getAlt().isNonVariant()) && VCFFilter.MIN_AF1 > 0 && Float.parseFloat(record.getInfoValue("AF1")) < VCFFilter.MIN_AF1)
           return false;
       }
       catch(NullPointerException npe){}