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Merge pull request #614 from broadinstitute/rp_fix_GenotypeGVCF_VCF_headers 

GenotypeGVCF was pulling the headers from all input rods including DBsnp...
This commit is contained in:
Eric Banks 2014-04-25 15:36:35 -04:00
parent 147ae21253 221b999cb0
commit 385fe5fb56
2 changed files with 7 additions and 7 deletions
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10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
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@ -154,8 +154,12 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
// create the annotation engine // create the annotation engine
annotationEngine = new VariantAnnotatorEngine(Arrays.asList("none"), annotationsToUse, Collections.<String>emptyList(), this, getToolkit()); annotationEngine = new VariantAnnotatorEngine(Arrays.asList("none"), annotationsToUse, Collections.<String>emptyList(), this, getToolkit());
// collect the actual rod bindings into a list for use later
for ( final RodBindingCollection<VariantContext> variantCollection : variantCollections )
variants.addAll(variantCollection.getRodBindings());
// take care of the VCF headers // take care of the VCF headers
final Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()); final Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), variants);
final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);
headerLines.addAll(annotationEngine.getVCFAnnotationDescriptions()); headerLines.addAll(annotationEngine.getVCFAnnotationDescriptions());
VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.MLE_ALLELE_COUNT_KEY, VCFConstants.MLE_ALLELE_FREQUENCY_KEY); VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.MLE_ALLELE_COUNT_KEY, VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
@ -168,10 +172,6 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
// create the genotyping engine // create the genotyping engine
genotypingEngine = new UnifiedGenotypingEngine(getToolkit(), new UnifiedArgumentCollection(), samples); genotypingEngine = new UnifiedGenotypingEngine(getToolkit(), new UnifiedArgumentCollection(), samples);
// collect the actual rod bindings into a list for use later
for ( final RodBindingCollection<VariantContext> variantCollection : variantCollections )
variants.addAll(variantCollection.getRodBindings());
} }
public VariantContext map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { public VariantContext map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {

2
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
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@ -102,7 +102,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference), " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
1, 1,
Arrays.asList("91061171c480901df8f776090527c182")); Arrays.asList("dc13542c71fbb4846507b0cdcc4827be"));
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec); executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
} }