public class GeneWiseMendelianAnnotationProcessor extends Object implements VariantContextProcessor
VariantContext
objects and annotate them with mendelian inheritance compatibility
The variants put into the processor must be clustered by contig name and sorted by begin positionConstructor and Description |
---|
GeneWiseMendelianAnnotationProcessor(Pedigree pedigree,
JannovarData jannovarData,
htsjdk.samtools.SAMSequenceDictionary seqDict,
Consumer<htsjdk.variant.variantcontext.VariantContext> sink)
Construct processor with the path to the PED file to use
|
Modifier and Type | Method and Description |
---|---|
void |
close()
Mark processing as done, no more variants will come in.
|
void |
extendHeader(htsjdk.variant.vcf.VCFHeader vcfHeader,
String prefix)
Appropriately extend
VCFHeader |
void |
put(htsjdk.variant.variantcontext.VariantContext vc)
Put a Variant Context into the filter.
|
public GeneWiseMendelianAnnotationProcessor(Pedigree pedigree, JannovarData jannovarData, htsjdk.samtools.SAMSequenceDictionary seqDict, Consumer<htsjdk.variant.variantcontext.VariantContext> sink)
pedigree
- the Pedigree
object to usejannovarData
- JannovarData
object to use for getting the genes fromseqDict
- SAMSequenceDictionary
to use for contig ordersink
- location to write the VariantContext
topublic void put(htsjdk.variant.variantcontext.VariantContext vc) throws VariantContextFilterException
VariantContextProcessor
put
in interface VariantContextProcessor
vc
- VariantContext
to put into the filter.VariantContextFilterException
- on problems during the filtrationpublic void close()
VariantContextProcessor
close
in interface VariantContextProcessor
close
in interface Closeable
close
in interface AutoCloseable
public void extendHeader(htsjdk.variant.vcf.VCFHeader vcfHeader, String prefix)
VCFHeader
Copyright © 2016. All rights reserved.