From b1ac4b81d5bd3dc03a796917ce60d8b0a66d0108 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 28 Dec 2009 17:28:51 +0000
Subject: [PATCH] Optimization: look up diploid genotypes from a static matrix
 instead of creating them on the fly (with String.format); bases no longer
 need to be ordered appropriately

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2448 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../DiploidGenotypeCalculationModel.java      |  4 +-
 .../sting/utils/genotype/DiploidGenotype.java | 37 +++++++++++--------
 2 files changed, 23 insertions(+), 18 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 1a1b205e1..d2f579eb1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
@@ -46,7 +46,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
             DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
             for ( char alt : BaseUtils.BASES ) {
                 if ( alt != ref ) {
-                    DiploidGenotype hetGenotype = DiploidGenotype.unorderedValueOf(ref, alt);
+                    DiploidGenotype hetGenotype = DiploidGenotype.createDiploidGenotype(ref, alt);
                     DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
                     AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], sample);
                 }
@@ -78,7 +78,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
         // set up some variables we'll need in the loop
         AlleleFrequencyMatrix matrix = AFMatrixMap.get(alt);
         DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
-        DiploidGenotype hetGenotype = DiploidGenotype.unorderedValueOf(ref, alt);
+        DiploidGenotype hetGenotype = DiploidGenotype.createDiploidGenotype(ref, alt);
         DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
 
         for ( String sample : GLs.keySet() ) {
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
index 51652d0cf..19117be2a 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.utils.genotype;
 
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.BaseUtils;
 
 /**
  * Created by IntelliJ IDEA.
@@ -53,28 +54,32 @@ public enum DiploidGenotype {
      * @return the diploid genotype
      */
     public static DiploidGenotype createHomGenotype(char hom) {
-        hom = Character.toUpperCase(hom);
-        switch (hom) {
-            case 'A': return DiploidGenotype.AA;
-            case 'C': return DiploidGenotype.CC;
-            case 'G': return DiploidGenotype.GG;
-            case 'T': return DiploidGenotype.TT;
-        }
-        throw new IllegalArgumentException(hom + " is not a valid base character");
+        int index = BaseUtils.simpleBaseToBaseIndex(hom);
+        if ( index == -1 )
+            throw new IllegalArgumentException(hom + " is not a valid base character");
+        return conversionMatrix[index][index];
     }
 
     /**
-     * get the genotype, given a string of 2 chars which may not necessarily be ordered correctly
+     * create a diploid genotype, given 2 chars which may not necessarily be ordered correctly
      * @param base1 base1
      * @param base2 base2
      * @return the diploid genotype
      */
-    public static DiploidGenotype unorderedValueOf(char base1, char base2) {
-        if ( base1 > base2 ) {
-            char temp = base1;
-            base1 = base2;
-            base2 = temp;
-        }
-        return valueOf(String.format("%c%c", base1, base2));
+    public static DiploidGenotype createDiploidGenotype(char base1, char base2) {
+        int index1 = BaseUtils.simpleBaseToBaseIndex(base1);
+        if ( index1 == -1 )
+            throw new IllegalArgumentException(base1 + " is not a valid base character");
+        int index2 = BaseUtils.simpleBaseToBaseIndex(base2);
+        if ( index2 == -1 )
+            throw new IllegalArgumentException(base2 + " is not a valid base character");
+        return conversionMatrix[index1][index2];
     }
+
+    private static final DiploidGenotype[][] conversionMatrix = {
+            { DiploidGenotype.AA, DiploidGenotype.AC, DiploidGenotype.AG, DiploidGenotype.AT },
+            { DiploidGenotype.AC, DiploidGenotype.CC, DiploidGenotype.CG, DiploidGenotype.CT },
+            { DiploidGenotype.AG, DiploidGenotype.CG, DiploidGenotype.GG, DiploidGenotype.GT },
+            { DiploidGenotype.AT, DiploidGenotype.CT, DiploidGenotype.GT, DiploidGenotype.TT }
+    };
 }
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