Fixing genotype given alleles for indels. Only take the records that start at this locus.

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java

@@ -26,14 +26,12 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -58,25 +56,6 @@ 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, final RodBinding<VariantContext> allelesBinding) {
-        if ( tracker == null || ref == null || logger == null )
-            throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger);
-        VariantContext vc = null;
-
-        // search for usable record
-        for( final VariantContext vc_input : tracker.getValues(allelesBinding) ) {
-            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");
-                }
-            }
-        }
-
-        return vc;
-    }
-
     public Allele getLikelihoods(RefMetaDataTracker tracker,
                                  ReferenceContext ref,
                                  Map<String, AlignmentContext> contexts,
@@ -96,7 +75,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         if ( alternateAlleleToUse != null ) {
             bestAlternateAllele = alternateAlleleToUse.getBases()[0];
         } else if ( useAlleleFromVCF ) {
-            VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger, UAC.alleles);
+            VariantContext vc = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, ref.getLocus(), true, logger, UAC.alleles);
 
             // ignore places where we don't have a variant
             if ( vc == null )

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
@@ -36,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -233,7 +235,7 @@ 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 ) {
-            VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger, UAC.alleles);
+            VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
             if ( vcInput == null )
                 return null;
             vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles(), InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, ref.getBase());
@@ -633,7 +635,7 @@ public class UnifiedGenotyperEngine {
             // no extended event pileup
             // if we're genotyping given alleles and we have a requested SNP at this position, do SNP
             if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
-                VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger, UAC.alleles);
+                VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
                 if (vcInput == null)
                     return null;
 
@@ -739,4 +741,24 @@ public class UnifiedGenotyperEngine {
 
         return afcm;
     }
+
+    public static VariantContext getVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc, boolean requireSNP, Logger logger, final RodBinding<VariantContext> allelesBinding) {
+        if ( tracker == null || ref == null || logger == null )
+            throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger);
+        VariantContext vc = null;
+
+        // search for usable record
+        for( final VariantContext vc_input : tracker.getValues(allelesBinding, loc) ) {
+            //System.out.println(vc_input);
+            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 in the alleles input file at site " + ref.getLocus() + ", only considering the first record");
+                }
+            }
+        }
+
+        return vc;
+    }
 }