From e88bc753aab863add25a79f222a7e83abcf4a8c1 Mon Sep 17 00:00:00 2001
From: Alec Wysoker <alecw@broadinstitute.org>
Date: Thu, 7 Feb 2013 11:58:41 -0500
Subject: [PATCH] Replace with map.containsKey followed by map.get with map.get
 followed by null check.

---
 .../gatk/walkers/compression/reducereads/ReduceReads.java  | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

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<LinkedList<GATKSAMRecord>, 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++;