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Updating the multi-step UG integration test.

This commit is contained in:
Ryan Poplin 2012-10-15 22:30:01 -04:00
parent cb33f25bfc
commit d27ae67bb6
2 changed files with 4 additions and 2 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
View File

@ -348,12 +348,14 @@ public class LikelihoodCalculationEngine {
} }
} }
} }
// add all filtered reads to the NO_CALL list because they weren't given any likelihoods // add all filtered reads to the NO_CALL list because they weren't given any likelihoods
for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) { for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) {
// only count the read if it overlaps the event, otherwise it is not added to the output read list at all // only count the read if it overlaps the event, otherwise it is not added to the output read list at all
if( callLoc.overlapsP(parser.createGenomeLoc(read)) ) { if( callLoc.overlapsP(parser.createGenomeLoc(read)) ) {
for( final Allele a : call.getFirst().getAlleles() ) for( final Allele a : call.getFirst().getAlleles() ) {
likelihoodMap.add(read, a, 0.0); likelihoodMap.add(read, a, 0.0);
}
} }
} }

2
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -349,7 +349,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("beee9457d7cea42006ac45400db5e873")); Arrays.asList("f3ff7fe0f15f31eadd726c711d6bf3de"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
} }