From 7104a3a96ccc84bad78b8b722ea94dc2e6be2296 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 5 Mar 2010 01:04:08 +0000
Subject: [PATCH] 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
---
 .../sting/gatk/executive/Accumulator.java             |  2 +-
 .../gatk/walkers/coverage/DepthOfCoverageWalker.java  | 11 +++++++++++
 .../gatk/walkers/DepthOfCoverageIntegrationTest.java  | 10 +++++++++-
 3 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
index d24242613..c120decd0 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
+++ b/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 );
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index 58ba3f499..3abb9669e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/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);    
+        }
+
     }
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
index f9b2edc69..d8fd749f5 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
@@ -45,5 +45,13 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
                 1, // just one output file
                 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);        
+    }
 }
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