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Bug fix in MLEAC calculation for when the exact model says the greedy AC of the alternate allele is zero.

This commit is contained in:
Ryan Poplin 2012-06-22 12:38:48 -04:00
parent 457d781029
commit 735b59d942
2 changed files with 3 additions and 2 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -316,6 +316,7 @@ public class UnifiedGenotyperEngine {
// if in GENOTYPE_GIVEN_ALLELES mode, we still want to allow the use of a poor allele // if in GENOTYPE_GIVEN_ALLELES mode, we still want to allow the use of a poor allele
else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
myAlleles.add(alternateAllele); myAlleles.add(alternateAllele);
alleleCountsofMLE.add(AFresult.getAlleleCountsOfMLE()[indexOfAllele-1]);
} }
} }

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

@ -44,7 +44,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn2() { public void testWithAllelesPassedIn2() {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("42c4e37e0f130dc796231003638a197c")); Arrays.asList("055012eca193a1f12421ea79bef1f4e0"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
} }
@ -327,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("c9b468fe75e7215a6d6d5a050af07918")); Arrays.asList("ebba1c06555c469cfb01d87f34aa6783"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
} }