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Don't print out alt alleles for ref calls 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5060 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-23 06:33:31 +00:00
parent 2ba35dc7ba
commit 2d4bcb60a1
2 changed files with 9 additions and 3 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -378,8 +378,14 @@ public class UnifiedGenotyperEngine {
int endLoc = calculateEndPos(vc.getAlleles(), vc.getReference(), loc);
Set<Allele> myAlleles = vc.getAlleles();
// strip out the alternate allele if it's a ref call
if ( bestAFguess == 0 ) {
myAlleles = new HashSet<Allele>(1);
myAlleles.add(vc.getReference());
}
VariantContext vcCall = new VariantContext("UG_call", loc.getContig(), loc.getStart(), endLoc,
vc.getAlleles(), genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);
myAlleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);
if ( annotationEngine != null ) {
// first off, we want to use the *unfiltered* context for the annotations

4
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -105,8 +105,8 @@ public class
@Test
public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "683ce57f2fd3acd5f6fe7599c1ace169" );
e.put( "-all_bases", "2ddf763c208602693cad942c9ccb804c" );
e.put( "-genotype", "4ffcb1e1f20ce175783c32c30deef8db" );
e.put( "-all_bases", "3d98205a31a133c11e518e095dc7ab65" );
e.put( "--min_base_quality_score 26", "5f1cfb9c7f82e6414d5db7aa344813ac" );
e.put( "--min_mapping_quality_score 26", "6c3ad441f3a23ade292549b1dea80932" );
e.put( "--max_mismatches_in_40bp_window 5", "5ecaf4281410b67e8e2e164f2ea0d58a" );