From 3ca3fd4b3e83922c4c0959d650119597e29b5702 Mon Sep 17 00:00:00 2001
From: Ami Levy-Moonshine <ami@broadinstitute.org>
Date: Fri, 21 Dec 2012 11:06:12 -0500
Subject: [PATCH] keep working on loglessHMM in UG

---
 .../sting/gatk/walkers/indels/PairHMMIndelErrorModel.java     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 737c24fb7..b45b396e2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -335,6 +335,7 @@ public class PairHMMIndelErrorModel {
                     getContextHomopolymerLength(readBases,hrunProfile);
                     fillGapProbabilities(hrunProfile, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities);
 
+                    boolean firstHap = true;
                     for (Allele a: haplotypeMap.keySet()) {
 
                         Haplotype haplotype = haplotypeMap.get(a);
@@ -374,7 +375,7 @@ public class PairHMMIndelErrorModel {
                         readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
                                 (read.hasBaseIndelQualities() ? read.getBaseInsertionQualities() : contextLogGapOpenProbabilities),
                                 (read.hasBaseIndelQualities() ? read.getBaseDeletionQualities() : contextLogGapOpenProbabilities),
-                                contextLogGapContinuationProbabilities, startIndexInHaplotype, previousHaplotypeSeen == null);
+                                contextLogGapContinuationProbabilities, startIndexInHaplotype, firstHap);
 
 
                         if (DEBUG) {
@@ -386,6 +387,7 @@ public class PairHMMIndelErrorModel {
 
                         perReadAlleleLikelihoodMap.add(p, a, readLikelihood);
                         readLikelihoods[readIdx][j++] = readLikelihood;
+                        firstHap = false;
                     }
                 }
             }