From 6bb864da2a7941caaebb0de351cb488164b69a7c Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 30 Nov 2009 22:29:07 +0000
Subject: [PATCH] More misc cleanup.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2191 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/recalibration/CycleCovariate.java | 7 ++++---
 .../gatk/walkers/recalibration/MinimumNQSCovariate.java  | 9 +++++----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
index 6b9ebe5b5..fa53248d9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
@@ -78,11 +78,12 @@ public class CycleCovariate implements Covariate {
         else if( read.getReadGroup().getPlatform().contains( "454" ) ) { // Some bams have "LS454" and others have just "454"
             int cycle = 0;
             //BUGBUG: should reverse directions on negative strand reads!
-            byte prevBase = read.getReadBases()[0];
+            byte[] bases = read.getReadBases();
+            byte prevBase = bases[0];
             for( int iii = 1; iii <= offset; iii++ ) {
-                if(read.getReadBases()[iii] != prevBase) { // This base doesn't match the previous one so it is a new cycle
+                if( bases[iii] != prevBase ) { // This base doesn't match the previous one so it is a new cycle
                     cycle++;
-                    prevBase = read.getReadBases()[iii];
+                    prevBase = bases[iii];
                 }
             }
             return cycle;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
index ef7855c39..a396ac8c5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
@@ -49,12 +49,13 @@ public class MinimumNQSCovariate implements Covariate {
     public final Comparable getValue( final SAMRecord read, final int offset ) {
     	
     	// Loop over the list of base quality scores in the window and find the minimum
-        int minQual = read.getBaseQualities()[offset];
+        byte[] quals = read.getBaseQualities();
+        int minQual = quals[offset];
         int minIndex = Math.max(offset - windowReach, 0);
-        int maxIndex = Math.min(offset + windowReach, read.getBaseQualities().length - 1);
+        int maxIndex = Math.min(offset + windowReach, quals.length - 1);
         for ( int iii = minIndex; iii < maxIndex; iii++ ) {
-            if( read.getBaseQualities()[iii] < minQual ) {
-                minQual = read.getBaseQualities()[iii];
+            if( quals[iii] < minQual ) {
+                minQual = quals[iii];
             }
         }
         return minQual;