diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index cd3255a78..b94baf931 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -627,9 +627,10 @@ public class ReduceReads extends ReadWalker, ReduceRea private void compressReadName(GATKSAMRecord read) { String name = read.getReadName(); String compressedName = read.isReducedRead() ? "C" : ""; - if (readNameHash.containsKey(name)) - compressedName += readNameHash.get(name).toString(); - else { + final Long readNumber = readNameHash.get(name); + if (readNumber != null) { + compressedName += readNumber.toString(); + } else { readNameHash.put(name, nextReadNumber); compressedName += nextReadNumber.toString(); nextReadNumber++;