Class GeneWiseMendelianAnnotationProcessor
- java.lang.Object
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- de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor
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- All Implemented Interfaces:
VariantContextProcessor
,Closeable
,AutoCloseable
public class GeneWiseMendelianAnnotationProcessor extends Object implements VariantContextProcessor
ProcessVariantContext
objects and annotate them with mendelian inheritance compatibilityThe variants put into the processor must be clustered by contig name and sorted by begin position
- Author:
- Manuel Holtgrewe
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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
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Method Summary
All Methods Instance Methods Concrete Methods 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 extendVCFHeader
void
put(htsjdk.variant.variantcontext.VariantContext vc)
Put a Variant Context into the filter.
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Constructor Detail
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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
- thePedigree
object to usejannovarData
-JannovarData
object to use for getting the genes fromsink
- location to write theVariantContext
tointerpretFilters
- whether or not to interpret genotype- or variant-wise filters
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Method Detail
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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 interfaceVariantContextProcessor
- Parameters:
vc
-VariantContext
to put into the filter.- Throws:
VariantContextFilterException
- on problems during the filtration
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close
public void close()
Description copied from interface:VariantContextProcessor
Mark processing as done, no more variants will come in.- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfaceVariantContextProcessor
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extendHeader
public void extendHeader(htsjdk.variant.vcf.VCFHeader vcfHeader, String prefix)
Appropriately extendVCFHeader
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