diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index 57a01c20a..5e78e3e0e 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -974,11 +974,11 @@ public class SAMDataSource { } } else { - // Unmapped read filter; just check getReadUnmappedFlag(). - if(!candidateRead.getReadUnmappedFlag()) - continue; - nextRead = candidateRead; - break; + // Found an unmapped read. We're done. + if(candidateRead.getReadUnmappedFlag()) { + nextRead = candidateRead; + break; + } } // No more reads available. Stop the search.