From db1f9af679aaf4a5821f8afda7b7f4a1dbe7923a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 12 May 2011 17:36:27 +0000
Subject: [PATCH] Now supports multiple records in allele at sites that
 genotype as reference

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5796 348d0f76-0448-11de-a6fe-93d51630548a
---
 ...NPGenotypeLikelihoodsCalculationModel.java | 30 +++++++++++--------
 .../genotyper/UnifiedGenotyperEngine.java     |  4 +--
 2 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index ae5c81642..59e339376 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -54,6 +54,23 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
     }
 
+    public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger) {
+        VariantContext vc = null;
+
+        // search for usable record
+        for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", null, ref.getLocus(), true, false) ) {
+            if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) {
+                if ( vc == null ) {
+                    vc = vc_input;
+                } else {
+                    logger.warn("Multiple valid VCF records detected at site " + ref.getLocus() + ", only considering alleles from first record only");
+                }
+            }
+        }
+
+        return vc;
+    }
+
     public Allele getLikelihoods(RefMetaDataTracker tracker,
                                  ReferenceContext ref,
                                  Map<String, AlignmentContext> contexts,
@@ -73,18 +90,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         if ( alternateAlleleToUse != null ) {
             bestAlternateAllele = alternateAlleleToUse.getBases()[0];
         } else if ( useAlleleFromVCF ) {
-            VariantContext vc = null;
-
-            // search for usable record
-            for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", null, ref.getLocus(), true, false) ) {
-                if ( vc_input != null && ! vc_input.isFiltered() && vc_input.isSNP() ) {
-                    if ( vc == null ) {
-                        vc = vc_input;
-                    } else {
-                        logger.warn("Multiple valid VCF records detected at site " + ref.getLocus() + ", only considering alleles from first record only");
-                    }
-                }
-            }
+            VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger);
 
             // ignore places where we don't have a variant
             if ( vc == null )
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 095b51fe9..d7b611759 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -198,8 +198,8 @@ public class UnifiedGenotyperEngine {
     private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
         VariantContext vc;
         if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
-            final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
-            if ( vcInput == null || vcInput.isFiltered() )
+            VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger);
+            if ( vcInput == null )
                 return null;
             vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
         } else {