Traversal now says 'done with mapped reads' instead of 'done' so we don't confuse users when there are a lot of unmapped reads left to process.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5577 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java

@@ -288,7 +288,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
 //                    else
 //                        logger.info(String.format("Processing %s", common));
                     logger.info(String.format("%15s        %5.2e %s     %s     %4.1f%%      %s  %s",
-                            loc == null ? "done" : loc, nRecords*1.0, elapsed, unitRate,
+                            loc == null ? "done with mapped reads" : loc, nRecords*1.0, elapsed, unitRate,
                             100*fractionGenomeTargetCompleted, estTotalRuntime, timeToCompletion));
 
                 }