ignore sequence-region lines that cannot be parsed

uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java

@@ -106,16 +106,25 @@ public class IndexedGFFDocumentEntry implements DocumentEntry
       int cnt = 0;
       while( (ln = in.readLine()) != null && ln.startsWith("#"))
       {
+        // ##sequence-region seqid start end
         if(ln.startsWith("##sequence-region "))
         {
           logger4j.debug(ln);
           final String parts[] = ln.split(" ");
 
-          //sequenceNames[cnt++] = parts[1];
+          try
+          {
             contigHash.put(parts[1], new IndexContig(parts[1], 1, Integer.parseInt(parts[3]), offset));
             offset+=Integer.parseInt(parts[3]);
             cnt++;
           }
+          catch(Exception ae)
+          {
+            contigHash.clear();
+            cnt = 0;
+            break;
+          }
+        }
       }
       in.close();
       
@@ -289,7 +298,12 @@ public class IndexedGFFDocumentEntry implements DocumentEntry
     if(!combinedReference)
     {
       if(contig != null)
+      {
+        if(contigHash.get(contig) == null)
+          System.err.println(contig+" not found in "+this.getName());
+        else
           list.add(contigHash.get(contig));
+      }
       else
         list.add(contigHash.get(sequenceNames[0]));
       return list;