// ///// end of hts bits.
+ /**
+ * Reads the contig with the given id and returns as a Jalview SequenceI
+ * object. Note the database must be indexed for this operation to succeed.
+ *
+ * @param id
+ * @return
+ */
public SequenceI getSequenceProxy(String id)
{
- if (!isValid())
+ if (!isValid() || !refFile.isIndexed())
{
+ System.err.println(
+ "Cannot read contig as file is invalid or not indexed");
return null;
}