fixes bug in gga mode caused by split multallic sites with genotypes

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerGenotypingEngine.java

@@ -180,7 +180,8 @@ protected static List<VariantContext> getVariantContextsFromGivenAlleles(final i
                     //TODO: how about replace it by vcSourceName = String.parseInt(nameCounter++)?
                     final String vcSourceName = "Comp" + givenAlleleSourceCount + "Allele" + alleleCount;
                     // check if this event is already in the list of events due to a repeat in the input alleles track
-                    final VariantContext candidateEventToAdd = new VariantContextBuilder(givenAlleleVC).alleles(alleleSet).source(vcSourceName).make();
+                    final VariantContext candidateEventToAdd = new VariantContextBuilder(givenAlleleVC).alleles(alleleSet)
+                            .genotypes(GenotypesContext.NO_GENOTYPES).source(vcSourceName).make();
 
                     final LocationAndAlleles locationAndAlleles = new LocationAndAlleles(candidateEventToAdd.getStart(), candidateEventToAdd.getAlleles());
                     if (! uniqueLocationsAndAlleles.contains(locationAndAlleles)) {

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerGenotypingEngineUnitTest.java

@@ -1,9 +1,7 @@
 package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
 
 import com.google.common.collect.Maps;
-import htsjdk.variant.variantcontext.Allele;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.variantcontext.VariantContextBuilder;
+import htsjdk.variant.variantcontext.*;
 import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.utils.haplotype.EventMap;
 import org.broadinstitute.hellbender.utils.haplotype.Haplotype;
@@ -159,6 +157,10 @@ public Object[][] getVcsAtThisLocationFromGivenAllelesData() {
         final VariantContext sameLocInsVc1 = new VariantContextBuilder("a", "20", 10093568, 10093568, sameLocInsAlleles1).make();
         sameLocInsHap1.setEventMap(new EventMap(Arrays.asList(sameLocInsVc1)));
 
+        final VariantContextBuilder deletionVCBuilderWithGts = new VariantContextBuilder("a", "20", 995, 1005, deletionAlleles)
+                .genotypes(new GenotypeBuilder("TEST", Arrays.asList(deletionAlleles.get(0), deletionAlleles.get(1))).make());
+        final VariantContext deletionVcWithGts = deletionVCBuilderWithGts.make();
+
         tests.add(new Object[]{1000, Arrays.asList(snpVc), Arrays.asList(snpVCBuilder.source("Comp0Allele0").make())});
         tests.add(new Object[]{995, Arrays.asList(deletionVc), Arrays.asList(deletionVCBuilder.source("Comp0Allele0").make())});
         tests.add(new Object[]{1000, Arrays.asList(deletionVc), Arrays.asList(deletionVCBuilder.source("Comp0Allele0").make())});
@@ -168,6 +170,9 @@ public Object[][] getVcsAtThisLocationFromGivenAllelesData() {
         tests.add(new Object[]{1000, Arrays.asList(deletionVc, deletionVcFalseDuplicate, deletionVcNoSpan),
                 Arrays.asList(deletionVCBuilder.source("Comp0Allele0").make(), deletionFalseDuplicateBuilder.source("Comp1Allele0").make())});
 
+        tests.add(new Object[]{1000, Arrays.asList(deletionVcWithGts, snpVc),
+                Arrays.asList(deletionVCBuilder.source("Comp0Allele0").make(), snpVCBuilder.source("Comp1Allele0").make())});
+
         return tests.toArray(new Object[][]{});
     }
 

src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf

@@ -32,3 +32,4 @@
 20	10004771	.	A	*,T	998.77	.	AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.270;DP=74;ExcessHet=3.0103;FS=2.397;MLEAC=1,0;MLEAF=0.500,0.00;MQ=51.81;MQRankSum=-6.325;QD=16.93;ReadPosRankSum=2.185;SOR=1.115	GT:AD:DP:GQ:PL	0/1:32,27,0:59:99:1027,0,1345,1162,1305,2852
 20	10006819	.	AAAAC	T	0	LowQual	AC=0;AF=0.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=61.14;SOR=0.572	GT:AD:DP:GQ:PL	0/0:75,0:75:99:0,244,2147483647
 20	10006823	.	C	*,G	0	LowQual	AC=0,0;AF=0.00,0.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=0,0;MLEAF=0.00,0.00;MQ=61.18;SOR=0.069	GT:AD:DP:GQ:PL	0/0:17,0,0:17:51:0,229,2147483647,51,819,590
+20	10008738	.	GGTTTGTTT	GGTTTGTTTGTTT,GGTTTGTTTGTTTGTTT,G	0	LowQual	AC=0,0,0;AF=0.00,0.00,0.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=0,0,0;MLEAF=0.00,0.00,0.00;MQ=37.07;SOR=0.488	GT:AD:DP:GQ:PL	0/0:50,0,0,0:50:99:0,154,2147483647,154,2147483647,2147483647,154,2147483647,2147483647,2147483647

src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGenotypeGivenAllelesMode_givenAlleles.vcf

@@ -34,3 +34,5 @@
 20	10004771	.	A	T	.	.	.	GT	0|1
 20	10006819	.	AAAAC	T	.	.	.	GT	0|1
 20	10006823	.	C	G	.	.	.	GT	0|1
+20	10008738	.	G	GGTTT,GGTTTGTTT	.	PASS	.	GT	1|2
+20	10008738	.	GGTTTGTTT	G	.	PASS	.	GT	0|1