X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fhtsjdk%2FHtsContigDb.java;h=73d16745a22cb6447bdd04bfe86e1391a63ea17d;hb=947109cebef3e98693ffc0a70b5bffcbd32217e2;hp=729f658ba6cf457fd05a372e526772ad128b2793;hpb=d53f86449820b92534376bd383e92a083037ec90;p=jalview.git

diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index 729f658..73d1674 100644
--- a/src/jalview/ext/htsjdk/HtsContigDb.java
+++ b/src/jalview/ext/htsjdk/HtsContigDb.java
@@ -250,10 +250,19 @@ public class HtsContigDb
 
   // ///// 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;
     }