public final class DBVariantContextAnnotator extends Object
VariantContext
objects using databasesConstructor and Description |
---|
DBVariantContextAnnotator(DBAnnotationDriver driver,
DBAnnotationOptions options)
Initialize the annotator using the given
DBAnnotationDriver |
Modifier and Type | Method and Description |
---|---|
htsjdk.variant.variantcontext.VariantContext |
annotateVariantContext(htsjdk.variant.variantcontext.VariantContext vc)
Annotate one
VariantContext with information from a database |
void |
annotateVariantContexts(Collection<htsjdk.variant.variantcontext.VariantContext> vcs)
Convenience method for bulk-annotating multiple
VariantContext objects |
htsjdk.variant.vcf.VCFHeader |
extendHeader(htsjdk.variant.vcf.VCFHeader vcfHeader)
Extend VCF header with the
VCFHeaderExtender for the annotator |
public DBVariantContextAnnotator(DBAnnotationDriver driver, DBAnnotationOptions options)
DBAnnotationDriver
driver
- public htsjdk.variant.vcf.VCFHeader extendHeader(htsjdk.variant.vcf.VCFHeader vcfHeader)
VCFHeaderExtender
for the annotatorvcfHeader
- Extend VCF headervcfHeader
public htsjdk.variant.variantcontext.VariantContext annotateVariantContext(htsjdk.variant.variantcontext.VariantContext vc)
VariantContext
with information from a databasevc
- VariantContext
to annotateVariantContext
vc
public void annotateVariantContexts(Collection<htsjdk.variant.variantcontext.VariantContext> vcs)
VariantContext
objectsvcs
- Collection
of VariantContext
objects to annotateCopyright © 2016. All rights reserved.