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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.

This commit is contained in:
Eric Banks 2012-12-10 14:47:04 -05:00
parent ceb5431dcb
commit bdda63d973
2 changed files with 4 additions and 5 deletions
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7
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
View File

@ -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 ) {

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -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) {