From bdda63d9730182e5b0860ab00fb4ef5f0857b223 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 10 Dec 2012 14:47:04 -0500
Subject: [PATCH] Related bug fixes to GGA mode in the HC: some variants
 (especially MNPs) were causing problems because they don't have to start at
 the current location to match the allele being genotyped.  Fixed.

---
 .../gatk/walkers/haplotypecaller/GenotypingEngine.java     | 7 +++----
 .../haplotypecaller/HaplotypeCallerIntegrationTest.java    | 2 +-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index fee6c86f8..4d81d0010 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -33,7 +33,6 @@ import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -449,10 +448,10 @@ public class GenotypingEngine {
 
         final ArrayList<Haplotype> undeterminedHaplotypes = new ArrayList<Haplotype>(haplotypes.size());
         for( final Haplotype h : haplotypes ) {
-            if( h.getEventMap().get(loc) == null ) { // no event at this location so this is a reference-supporting haplotype
-                alleleMapper.get(refAllele).add(h);
-            } else if( h.isArtificialHaplotype() && loc == h.getArtificialAllelePosition() && alleleMapper.containsKey(h.getArtificialAllele()) ) {
+            if( h.isArtificialHaplotype() && loc == h.getArtificialAllelePosition() && alleleMapper.containsKey(h.getArtificialAllele()) ) {
                 alleleMapper.get(h.getArtificialAllele()).add(h);
+            } else if( h.getEventMap().get(loc) == null ) { // no event at this location so let's investigate later
+                undeterminedHaplotypes.add(h);
             } else {
                 boolean haplotypeIsDetermined = false;
                 for( final VariantContext vcAtThisLoc : eventsAtThisLoc ) {
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index e9c1ec605..a80137c27 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -33,7 +33,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
-                "e2b3bf420c45c677956a2e4a56d75ea2");
+                "fe84caa79f59ecbd98fcbcd5b30ab164");
     }
 
     private void HCTestComplexVariants(String bam, String args, String md5) {