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Annotate with FS even for filtered sites

This commit is contained in:
Eric Banks 2012-01-18 22:04:51 -05:00
parent b0b0cd9aef
commit ab8f499bc3
2 changed files with 3 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
View File

@ -54,7 +54,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
private static final double MIN_PVALUE = 1E-320; private static final double MIN_PVALUE = 1E-320;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) { public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( ! vc.isVariant() || vc.isFiltered() ) if ( !vc.isVariant() )
return null; return null;
int[][] table; int[][] table;

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 " + validationDataLocation + "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 " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("43e7a17d95b1a0cf72e669657794d802")); Arrays.asList("1899bdb956c62bbcbf160b18cd3aea60"));
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);
} }
@ -275,7 +275,7 @@ 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 "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + + validationDataLocation + "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("36ce53ae4319718ad9c8ae391deebc8c")); Arrays.asList("320f61c87253aba77d6dc782242cba8b"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
} }