From 9a1d0d7076853670dcace2dcd4e37a3d55d0566c Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 11 May 2011 14:17:14 +0000
Subject: [PATCH] Simple bug fix to allow multiple records at same site when
 genotyping given alleles.  Takes only the first record (respecting filters,
 SNP type, etc), and issues a warning if there is more than one valid record
 at a site

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5789 348d0f76-0448-11de-a6fe-93d51630548a
---
 ...NPGenotypeLikelihoodsCalculationModel.java | 26 +++++++++++++------
 1 file changed, 18 insertions(+), 8 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 54ce35bbd..ae5c81642 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -73,18 +73,28 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         if ( alternateAlleleToUse != null ) {
             bestAlternateAllele = alternateAlleleToUse.getBases()[0];
         } else if ( useAlleleFromVCF ) {
-            final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
-            if ( vcInput == null || vcInput.isFiltered() || !vcInput.isSNP() )
-                return null;
-            if ( !vcInput.isSNP() ) {
-                logger.info("Record at position " + ref.getLocus() + " is not a SNP; skipping...");
-                return null;
+            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");
+                    }
+                }
             }
-            if ( !vcInput.isBiallelic() ) {
+
+            // ignore places where we don't have a variant
+            if ( vc == null )
+                return null;
+
+            if ( !vc.isBiallelic() ) {
                 // for multi-allelic sites go back to the reads and find the most likely alternate allele
                 initializeBestAlternateAllele(refBase, contexts);
             } else {
-                bestAlternateAllele = vcInput.getAlternateAllele(0).getBases()[0];
+                bestAlternateAllele = vc.getAlternateAllele(0).getBases()[0];
             }
         } else {
             initializeBestAlternateAllele(refBase, contexts);