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The VariantContext utility method used by SelectVariants wasn't checking the filter status (unfiltered vs. passing filters) and always returned a VC that was passing filters. This is fixed and the md5 from the VCF Streaming test has been re-updated.

This commit is contained in:
Eric Banks 2011-06-30 15:26:09 -04:00
parent 867056af51
commit 761347b8d5
2 changed files with 3 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -414,7 +414,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @return vc subcontext
*/
public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes, Set<Allele> alleles) {
return new VariantContext(getSource(), contig, start, stop, alleles, genotypes, getNegLog10PError(), getFilters(), getAttributes());
return new VariantContext(getSource(), contig, start, stop, alleles, genotypes, getNegLog10PError(), filtersWereApplied() ? getFilters() : null, getAttributes());
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" --NO_HEADER" +
" -o %s",
1,
Arrays.asList("995c07ccd593fe1c35d0d28155112a55")
Arrays.asList("debbbf3e661b6857cc8d99ff7635bb1d")
);
executeTest("testSimpleVCFStreaming", spec);
@ -98,7 +98,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" -EV CompOverlap -noEV -noST" +
" -o %s",
1,
Arrays.asList("f60729c900bc8368717653b3fad80d1e")
Arrays.asList("f60729c900bc8368717653b3fad80d1e") //"f60729c900bc8368717653b3fad80d1e"
);
executeTest("testVCFStreamingChain", selectTestSpec);