Fix for accumulator exception when running reduce by interval walkers without

intervals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2935 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java

@@ -48,7 +48,7 @@ public abstract class Accumulator {
      * @return Accumulator suitable for this walker.s
      */
     public static Accumulator create( GenomeAnalysisEngine engine, Walker walker ) {
-        if( walker.isReduceByInterval() )
+        if( walker.isReduceByInterval() && engine.getIntervals() != null)
             return new IntervalAccumulator( walker, engine.getIntervals() );
         else
             return new StandardAccumulator( walker );

java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java

@@ -410,5 +410,16 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
             }
         }
 
+        @Override
+        public String toString() {
+            // This is an executive summary, included mainly so that integration tests will pass.
+            // TODO: Add a more compelling summary.
+            return String.format("Summary: total coverage = %d; # of deletions = %d; # of bad mapping quality reads = %d; minimum covered depth =%d",
+                    totalCoverage,
+                    numDeletions,
+                    numBadMQReads,
+                    minDepthCoveredLoci);    
+        }
+
     }
 }

java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java

@@ -46,4 +46,12 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
                 Arrays.asList("a332d1539b29dff615b198818a3d4dd1"));
         executeTest("testDepthOfCoverage454", spec);
     }
+
+    @Test
+    public void testDepthOfCoverageNoIntervals() {
+        WalkerTestSpec spec = new WalkerTestSpec( "-T DepthOfCoverage -R " + validationDataLocation + "human_b36_both.partial.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -o %s",
+                1, // just one output file
+                Arrays.asList("7b8fc75dd1995d270831b31c268392a5"));
+        executeTest("testDepthOfCoverageNoIntervals", spec);        
+    }
 }