From 284f83469b9ad7942c369d5fbd41fc36fc34ea0c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 6 Sep 2011 15:09:37 -0400
Subject: [PATCH] ReducedRead flag cached in GATKSAMRecord.  20% performance
 improvement

---
 .../sting/utils/pileup/PileupElement.java        |  2 +-
 .../sting/utils/sam/GATKSAMRecord.java           | 16 +++++++++++++++-
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
index 66e1afecb..12899e898 100755
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
@@ -82,7 +82,7 @@ public class PileupElement {
     // --------------------------------------------------------------------------
 
     private Integer getReducedReadQualityTagValue() {
-        return (Integer)getRead().getAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
+        return getRead().getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
     }
 
     public boolean isReducedRead() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index 517f9f75d..c55a462f1 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -41,6 +41,10 @@ public class GATKSAMRecord extends SAMRecord {
     // because some values can be null, we don't want to duplicate effort
     private boolean retrievedReadGroup = false;
 
+    /** A private cache for the reduced read quality.  Null indicates the value hasn't be fetched yet or isn't available */
+    private boolean lookedUpReducedReadQuality = false;
+    private Integer reducedReadQuality;
+
     // These temporary attributes were added here to make life easier for
     // certain algorithms by providing a way to label or attach arbitrary data to
     // individual GATKSAMRecords.
@@ -338,7 +342,17 @@ public class GATKSAMRecord extends SAMRecord {
 
     public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); }
 
-    public Integer getIntegerAttribute(final String tag) { return mRecord.getIntegerAttribute(tag); }
+    public Integer getIntegerAttribute(final String tag) {
+        if ( tag == ReadUtils.REDUCED_READ_QUALITY_TAG ) {
+            if ( ! lookedUpReducedReadQuality ) {
+                lookedUpReducedReadQuality = true;
+                reducedReadQuality = mRecord.getIntegerAttribute(tag);
+            }
+            return reducedReadQuality;
+        } else {
+            return mRecord.getIntegerAttribute(tag);
+        }
+    }
 
     public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); }