From fa9c21c020c960627738aba67347e16ef09072d5 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 1 Oct 2010 02:32:50 +0000
Subject: [PATCH] More fixes for exact AF calculation model in new unified
 genotyper: a) Fixed bugs in new dynamic programming-based genotyper b) Fixed
 up temp hack that handles extended pileups for now.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4398 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/ExactAFCalculationModel.java        | 15 +++++++++------
 .../walkers/genotyper/UnifiedGenotyperEngine.java |  3 ++-
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 3be8fc29e..43d74a055 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -134,8 +134,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
     protected Map<String, Genotype> generateCalls(Map<String, StratifiedAlignmentContext> contexts,
                                                   Map<String, BiallelicGenotypeLikelihoods> GLs,
                                                   int bestAFguess) {
-        // first experiment: refine do genotype assignment by Hardy Weinberg equilibrium assumption.
-        HashMap<String, Genotype> calls = new HashMap<String, Genotype>();
+         HashMap<String, Genotype> calls = new HashMap<String, Genotype>();
 
 
         double[][] pathMetricArray = new double[GLs.size()+1][bestAFguess+1];
@@ -144,6 +143,13 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         ArrayList<String> sampleIndices = new ArrayList<String>();
         int sampleIdx = 0;
 
+        // todo - optimize initialization
+        for (int k=0; k <= bestAFguess; k++)
+            for (int j=0; j <= GLs.size(); j++)
+                pathMetricArray[j][k] = -1e30;
+
+        pathMetricArray[0][0] = 0.0;
+
         if (SIMPLE_GREEDY_GENOTYPER) {
             sampleIndices.addAll(GLs.keySet());
             sampleIdx = GLs.size();
@@ -222,10 +228,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
             if (qual <= 0.0) {
                 qual = 0.0;
-                myAlleles.clear();
-                myAlleles.add(Allele.NO_CALL);
-                myAlleles.add(Allele.NO_CALL);
-            }
+             }
 
             attributes.put(VCFConstants.GENOTYPE_QUALITY_KEY,String.format("%4.2f", 10*qual));
 
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 c32fcd371..6214d0901 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
@@ -230,7 +230,8 @@ public class UnifiedGenotyperEngine {
         // todo - temp fix until we can deal with extended events properly
         //VariantContext vc = new VariantContext("UG_call", loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);
         VariantContext vc = new VariantContext("UG_call", loc.getContig(), loc.getStart(),
-                loc.getStart()+refAllele.length(), alleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);
+                Math.max(loc.getStart()+refAllele.length()-1,loc.getStart()),
+                alleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);
 
 
         if ( annotationEngine != null ) {