Merge pull request #140 from broadinstitute/dr_interval_intersection_bug_GSA-909

Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists

public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java

@@ -98,6 +98,7 @@ public final class IntervalBinding<T extends Feature> {
             intervals = IntervalUtils.parseIntervalArguments(genomeLocParser, stringIntervals);
         }
 
+        Collections.sort(intervals);
         return intervals;
     }
 

public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java

@@ -285,4 +285,20 @@ public class IntervalIntegrationTest extends WalkerTest {
                 Arrays.asList(md5));
         executeTest("testSymbolicAlleles", spec);
     }
+
+    @Test
+    public void testIntersectionOfLexicographicallySortedIntervals() {
+        final String md5 = "18be9375e5a753f766616a51eb6131f0";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                " -T CountLoci" +
+                " -I " + privateTestDir + "NA12878.4.snippet.bam" +
+                " -R " + b37KGReference +
+                " -L " + privateTestDir + "lexicographicallySortedIntervals.bed" +
+                " -L 4" +
+                " -isr INTERSECTION" +
+                " -o %s",
+                1, // just one output file
+                Arrays.asList(md5));
+        executeTest("testIntersectionOfLexicographicallySortedIntervals", spec);
+    }
 }