diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java index 4e567ed54..1c063230d 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java @@ -823,9 +823,12 @@ public class SAMDataSource implements SimpleDataSource { } } + // No more reads available. Stop the search. + if(!iterator.hasNext()) + break; + // No reasonable read found; advance the iterator. - if(iterator.hasNext()) - candidateRead = iterator.next(); + candidateRead = iterator.next(); } } }