From 72e496d6f37b8226e28244a4dc26fecabd8e45b8 Mon Sep 17 00:00:00 2001
From: Alec Wysoker <alecw@broadinstitute.org>
Date: Thu, 7 Feb 2013 11:57:43 -0500
Subject: [PATCH 1/2] Eliminate unnecessary zeroing out of primitive arrays
 immediately after new.

---
 .../walkers/compression/reducereads/BaseAndQualsCounts.java  | 5 +----
 .../gatk/walkers/compression/reducereads/BaseCounts.java     | 5 +----
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
index 207590c5f..7f8b0dded 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
@@ -60,10 +60,7 @@ public class BaseAndQualsCounts extends BaseCounts {
         super();
         this.sumInsertionQuals = new long[BaseIndex.values().length];
         this.sumDeletionQuals  = new long[BaseIndex.values().length];
-        for (final BaseIndex i : BaseIndex.values()) {
-            sumInsertionQuals[i.index] = 0L;
-            sumDeletionQuals[i.index] = 0L;
-        }
+        // Java primitive arrays comes zero-filled, so no need to do it explicitly.
     }
 
     public void incr(final byte base, final byte baseQual, final byte insQual, final byte delQual) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
index 67c8e68df..399cbd2a5 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
@@ -69,10 +69,7 @@ import com.google.java.contract.Requires;
     public BaseCounts() {
         counts = new int[BaseIndex.values().length];
         sumQuals = new long[BaseIndex.values().length];
-        for (final BaseIndex i : BaseIndex.values()) {
-            counts[i.index] = 0;
-            sumQuals[i.index] = 0L;
-        }
+        // Java primitive arrays comes zero-filled, so no need to do it explicitly.
     }
 
     public static BaseCounts createWithCounts(int[] countsACGT) {

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 2/2] 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++;