Package de.charite.compbio.jannovar.mendel.filter

Class GeneWiseMendelianAnnotationProcessor

java.lang.Object

de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor

All Implemented Interfaces:

VariantContextProcessor, Closeable, AutoCloseable

public class GeneWiseMendelianAnnotationProcessor
extends Object
implements VariantContextProcessor

Process 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 position

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
GeneWiseMendelianAnnotationProcessor(de.charite.compbio.jannovar.pedigree.Pedigree pedigree, de.charite.compbio.jannovar.data.JannovarData jannovarData, Consumer<htsjdk.variant.variantcontext.VariantContext> sink, boolean interpretFilters)	Construct processor with the path to the PED file to use

Method Summary

Modifier and Type	Method	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.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GeneWiseMendelianAnnotationProcessor

public GeneWiseMendelianAnnotationProcessor(de.charite.compbio.jannovar.pedigree.Pedigree pedigree,
                                            de.charite.compbio.jannovar.data.JannovarData jannovarData,
                                            Consumer<htsjdk.variant.variantcontext.VariantContext> sink,
                                            boolean interpretFilters)

Construct processor with the path to the PED file to use

Parameters:

pedigree - the Pedigree object to use

jannovarData - JannovarData object to use for getting the genes from

sink - location to write the VariantContext to

interpretFilters - whether or not to interpret genotype- or variant-wise filters

Method Detail

put

public void put(htsjdk.variant.variantcontext.VariantContext vc)
         throws VariantContextFilterException

Description copied from interface: VariantContextProcessor

Put a Variant Context into the filter.

Specified by:

put in interface VariantContextProcessor

Parameters:

vc - VariantContext to put into the filter.

Throws:

VariantContextFilterException - on problems during the filtration

close

public void close()

Description copied from interface: VariantContextProcessor

Mark processing as done, no more variants will come in.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface VariantContextProcessor

extendHeader

public void extendHeader(htsjdk.variant.vcf.VCFHeader vcfHeader,
                         String prefix)

Appropriately extend VCFHeader