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