From fd8351cd4969066479832bc547e4517b7cfdefc3 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 11 Oct 2010 04:04:07 +0000
Subject: [PATCH] Get rid of useless test/'optimization' that was carried over
 from UGv1.  New codde is (minimally) faster with same results.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4478 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/AlleleFrequencyCalculationModel.java    | 11 -----------
 .../walkers/genotyper/GridSearchAFEstimation.java     |  5 +----
 .../walkers/genotyper/UnifiedGenotyperEngine.java     |  7 -------
 3 files changed, 1 insertion(+), 22 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
index 33b7e0940..cc17e9104 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
@@ -61,8 +61,6 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
     protected Logger logger;
     protected PrintStream verboseWriter;
 
-    private int minAlleleFrequencyToTest;
-
     protected AlleleFrequencyCalculationModel(int N, Logger logger, PrintStream verboseWriter) {
         this.N = N;
         this.logger = logger;
@@ -109,15 +107,6 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
         return generateCalls(contexts, GLs, AFofMaxLikelihood);
     }
 
-    // TODO: get rid of this optimization, it is wrong!
-    protected int getMinAlleleFrequencyToTest() {
-        return minAlleleFrequencyToTest;
-    }
-
-    protected void setMinAlleleFrequencyToTest(int minAF) {
-        minAlleleFrequencyToTest = minAF;
-    }
-
     protected Map<String, Genotype> generateCalls(Map<String, StratifiedAlignmentContext> contexts,
                                                   Map<String, BiallelicGenotypeLikelihoods> GLs,
                                                   int frequency) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
index ee19d26aa..6977fb0d8 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
@@ -56,9 +56,6 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
         log10AlleleFrequencyPosteriors[0] = AFMatrix.getLikelihoodsOfFrequency() + log10AlleleFrequencyPriors[0];
         double maxLikelihoodSeen = log10AlleleFrequencyPosteriors[0];
 
-        // TODO: get rid of this optimization, it is wrong!
-        int minAlleleFrequencyToTest = getMinAlleleFrequencyToTest();
-
         int maxAlleleFrequencyToTest = AFMatrix.getSamples().size() * 2;
 
         // for each minor allele frequency, calculate log10PofDgivenAFi
@@ -71,7 +68,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
 
             // an optimization to speed up the calculation: if we are beyond the local maximum such
             //  that subsequent likelihoods won't factor into the confidence score, just quit
-            if ( i >= minAlleleFrequencyToTest && maxLikelihoodSeen - log10AlleleFrequencyPosteriors[i] > LOG10_OPTIMIZATION_EPSILON )
+            if ( maxLikelihoodSeen - log10AlleleFrequencyPosteriors[i] > LOG10_OPTIMIZATION_EPSILON )
                 return;
 
             if ( log10AlleleFrequencyPosteriors[i] > maxLikelihoodSeen )
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index f3a62719e..70929c268 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -142,10 +142,6 @@ public class UnifiedGenotyperEngine {
         if ( GLs.size() == 0 )
             return estimateReferenceConfidence(stratifiedContexts, genotypePriors.getHeterozygosity(), false);
 
-        // reset the optimization value and determine the p(AF>0)
-        // TODO: get rid of this optimization, it is wrong!
-        afcm.get().setMinAlleleFrequencyToTest(0);
-
         // 'zero' out the AFs (so that we don't have to worry if not all samples have reads at this position)
         clearAFarray(log10AlleleFrequencyPosteriors.get());
         afcm.get().getLog10PNonRef(tracker, refContext, GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.get());
@@ -221,9 +217,6 @@ public class UnifiedGenotyperEngine {
             double lod = overallLog10PofF - overallLog10PofNull;
             //System.out.println("overallLog10PofNull=" + overallLog10PofNull + ", overallLog10PofF=" + overallLog10PofF);
 
-            // set the optimization value for the subsequent strand calculations
-            afcm.get().setMinAlleleFrequencyToTest(bestAFguess);
-
             // the forward lod
             GLs.clear();
             glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.FORWARD, genotypePriors, GLs);