From ea4300d58373660a10c38750b3f74c2617f17db3 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 9 Apr 2012 13:45:17 -0400
Subject: [PATCH] Refactoring so that Unified Argument Collection doesn't use
 deprecated classes.

---
 ...ploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java | 2 ++
 .../gatk/walkers/genotyper/UnifiedArgumentCollection.java    | 4 ++--
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 5 +++--
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java
index 5f374e597..5d6cf9f7d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java
@@ -72,6 +72,8 @@ import static java.lang.Math.pow;
  */
 public class DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering implements Cloneable {
 
+    public final static double DEFAULT_PCR_ERROR_RATE = 1e-4;
+
     protected final static int FIXED_PLOIDY = 2;
     protected final static int MAX_PLOIDY = FIXED_PLOIDY + 1;
     protected final static double ploidyAdjustment = log10(FIXED_PLOIDY);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 58b8af493..9f606cdfb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -45,7 +45,7 @@ public class UnifiedArgumentCollection {
      * het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2
      */
     @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
-    public Double heterozygosity = DiploidSNPGenotypePriors.HUMAN_HETEROZYGOSITY;
+    public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY;
 
     /**
      * The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily
@@ -53,7 +53,7 @@ public class UnifiedArgumentCollection {
      * effectively acts as a cap on the base qualities.
      */
     @Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false)
-    public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;
+    public Double PCR_error = DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.DEFAULT_PCR_ERROR_RATE;
 
     /**
      * Specifies how to determine the alternate allele to use for genotyping
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 5d926a865..9241482d4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -53,6 +53,9 @@ public class UnifiedGenotyperEngine {
     
     public static final int DEFAULT_PLOIDY = 2;
 
+    public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3;
+    public static final double HUMAN_INDEL_HETEROZYGOSITY = 1e-4;
+
     public enum OUTPUT_MODE {
         /** produces calls only at variant sites */
         EMIT_VARIANTS_ONLY,
@@ -622,8 +625,6 @@ public class UnifiedGenotyperEngine {
 
     }
 
-    public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3;
-    public static final double HUMAN_INDEL_HETEROZYGOSITY = 1e-4;
     protected double getTheta( final GenotypeLikelihoodsCalculationModel.Model model ) {
         if( model.name().contains("SNP") )
             return HUMAN_SNP_HETEROZYGOSITY;