From cb6d6f268613d924a0e60a153bc0ebf3739c6330 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Nov 2009 05:21:07 +0000
Subject: [PATCH] Very minor performance improvements

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2137 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/DiploidGenotypeCalculationModel.java       | 2 +-
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java   | 9 +++++----
 .../sting/utils/genotype/DiploidGenotype.java            | 6 +++---
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
index 672689eab..efa006596 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
@@ -43,9 +43,9 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
             double[] posteriors = GL.getPosteriors();
 
             // for each alternate allele, fill the matrix
+            DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
             for ( char alt : BaseUtils.BASES ) {
                 if ( alt != ref ) {
-                    DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
                     DiploidGenotype hetGenotype = ref < alt ? DiploidGenotype.valueOf(String.valueOf(ref) + String.valueOf(alt)) : DiploidGenotype.valueOf(String.valueOf(alt) + String.valueOf(ref));
                     DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
                     AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], index);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 36f56c3e7..9a6f7c03b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -185,13 +185,14 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
     private AlignmentContext filterAlignmentContext(AlignmentContext context) {
         List<SAMRecord> reads = context.getReads();
         List<Integer> offsets = context.getOffsets();
+        int numReads = reads.size();
 
-        List<SAMRecord> newReads = new ArrayList<SAMRecord>();
-        List<Integer> newOffsets = new ArrayList<Integer>();
+        List<SAMRecord> newReads = new ArrayList<SAMRecord>(numReads);
+        List<Integer> newOffsets = new ArrayList<Integer>(numReads);
 
-        for (int i = 0; i < reads.size(); i++) {
+        for (int i = 0; i < numReads; i++) {
             SAMRecord read = reads.get(i);
-            if ( read.getMappingQuality() != 0 ) {
+            if ( read.getMappingQuality() > 0 ) {
                 newReads.add(read);
                 newOffsets.add(offsets.get(i));
             }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
index 6c1102c9f..3ff34ab22 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
@@ -28,11 +28,11 @@ public enum DiploidGenotype {
     }
 
     public boolean isHomRef(char r) {
-        return isHom() && r == this.toString().charAt(0);
+        return isHom() && r == base1;
     }
 
     public boolean isHomVar(char r) {
-        return isHom() && r != this.toString().charAt(0);
+        return isHom() && r != base1;
     }
 
     public boolean isHetRef(char r) {
@@ -59,7 +59,7 @@ public enum DiploidGenotype {
      * @return the diploid genotype
      */
     public static DiploidGenotype createHomGenotype(char hom) {
-        return DiploidGenotype.valueOf((String.valueOf(hom) + String.valueOf(hom)).toUpperCase());     
+        return DiploidGenotype.valueOf((String.valueOf(hom) + String.valueOf(hom)).toUpperCase());
     }
 
     /**