catch ArrayIndexOutOfBoundsException thrown by tabix when reference is not found

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16203 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

@@ -64,7 +64,16 @@ public abstract class AbstractVCFReader
     else
     {
       if(tabixIterator == null)
-        tabixIterator = ((TabixReader)this).query(chr+":"+sbeg+"-"+send);
+      {
+        try
+        {
+          tabixIterator = ((TabixReader)this).query(chr+":"+sbeg+"-"+send);
+        }
+        catch(ArrayIndexOutOfBoundsException aob)
+        {
+          System.err.println(chr+":"+sbeg+"-"+send+" not found in "+((TabixReader)this).getFileName());
+        }
+      }
       if(tabixIterator == null)
         return null;