org.broadinstitute.hellbender.tools.copynumber.gcnv

Class GermlineCNVSegmentVariantComposer

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer<IntegerCopyNumberSegment>

org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer

public final class GermlineCNVSegmentVariantComposer
extends GermlineCNVVariantComposer<IntegerCopyNumberSegment>

Helper class for PostprocessGermlineCNVCalls for single-sample postprocessing of segmented GermlineCNVCaller calls.

Field Summary

Fields inherited from class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer

outputWriter, sampleName

Constructor Summary

Constructors

Constructor and Description
GermlineCNVSegmentVariantComposer(htsjdk.variant.variantcontext.writer.VariantContextWriter outputWriter, java.lang.String sampleName, IntegerCopyNumberState refAutosomalCopyNumberState, java.util.Set<java.lang.String> allosomalContigSet) Constructor.

Method Summary

Modifier and Type	Method and Description
void	composeVariantContextHeader(htsjdk.samtools.SAMSequenceDictionary sequenceDictionary, java.util.Set<htsjdk.variant.vcf.VCFHeaderLine> vcfDefaultToolHeaderLines) Compose the header of the variant context.

Methods inherited from class org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer

writeAll

Methods inherited from class java.lang.Object

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

Constructor Detail

GermlineCNVSegmentVariantComposer

public GermlineCNVSegmentVariantComposer(htsjdk.variant.variantcontext.writer.VariantContextWriter outputWriter,
                                         java.lang.String sampleName,
                                         IntegerCopyNumberState refAutosomalCopyNumberState,
                                         java.util.Set<java.lang.String> allosomalContigSet)

Constructor.

Parameters:

outputWriter - variant context writer

sampleName - sample name

refAutosomalCopyNumberState - ref copy-number state on autosomal contigs

allosomalContigSet - set of allosomal contigs (ref copy-number allele be chosen according to given contig baseline copy-number states)

Method Detail

composeVariantContextHeader

public void composeVariantContextHeader(htsjdk.samtools.SAMSequenceDictionary sequenceDictionary,
                                        java.util.Set<htsjdk.variant.vcf.VCFHeaderLine> vcfDefaultToolHeaderLines)

Description copied from class: GermlineCNVVariantComposer

Compose the header of the variant context.

Parameters:

sequenceDictionary - sequence dictionary to use for contig header lines

vcfDefaultToolHeaderLines - default header lines of the VCF generation tool