belated special case fix for Menachem; if the results of a BTI and BTIMR produce an empty interval list, exception out. This would be solved long term with better handling or empty and / or null interval lists. I'll add a JIRA

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4754 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java

@@ -113,6 +113,10 @@ public class IntervalUtils {
                 else iTwo++;
             }
 
+        //if we have an empty list, throw an exception.  If they specified intersection and there are no items, this is bad.
+        if (retList == null || retList.size() == 0)
+                throw new UserException.BadInput("The INTERSECTION of your -BTI and -L options produced no intervals.");
+
         // we don't need to add the rest of remaining locations, since we know they don't overlap. return what we have
         return retList;
     }

java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java

@@ -31,7 +31,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
         genomeLocParser = new GenomeLocParser(seq);
     }
 
-    @Test
+    @Test(expectedExceptions=UserException.class)
     public void testMergeListsBySetOperatorNoOverlap() {
         // a couple of lists we'll use for the testing
         List<GenomeLoc> listEveryTwoFromOne = new ArrayList<GenomeLoc>();