org.broadinstitute.hellbender.tools.spark.sv.discovery

Class SvDiscoveryInputMetaData.SampleSpecificData

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData

Enclosing class:

SvDiscoveryInputMetaData

public static final class SvDiscoveryInputMetaData.SampleSpecificData
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
SampleSpecificData(java.lang.String sampleId, org.apache.spark.broadcast.Broadcast<SVIntervalTree<htsjdk.variant.variantcontext.VariantContext>> cnvCallsBroadcast, java.util.List<SVInterval> assembledIntervals, PairedStrandedIntervalTree<EvidenceTargetLink> evidenceTargetLinks, ReadMetadata readMetadata, org.apache.spark.broadcast.Broadcast<htsjdk.samtools.SAMFileHeader> headerBroadcast)

Method Summary

Modifier and Type	Method and Description
java.util.List<SVInterval>	getAssembledIntervals()
org.apache.spark.broadcast.Broadcast<SVIntervalTree<htsjdk.variant.variantcontext.VariantContext>>	getCnvCallsBroadcast()
PairedStrandedIntervalTree<EvidenceTargetLink>	getEvidenceTargetLinks()
org.apache.spark.broadcast.Broadcast<htsjdk.samtools.SAMFileHeader>	getHeaderBroadcast()
ReadMetadata	getReadMetadata()
java.lang.String	getSampleId()

Methods inherited from class java.lang.Object

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

Constructor Detail

SampleSpecificData

public SampleSpecificData(java.lang.String sampleId,
                          org.apache.spark.broadcast.Broadcast<SVIntervalTree<htsjdk.variant.variantcontext.VariantContext>> cnvCallsBroadcast,
                          java.util.List<SVInterval> assembledIntervals,
                          PairedStrandedIntervalTree<EvidenceTargetLink> evidenceTargetLinks,
                          ReadMetadata readMetadata,
                          org.apache.spark.broadcast.Broadcast<htsjdk.samtools.SAMFileHeader> headerBroadcast)

Method Detail

getSampleId

public java.lang.String getSampleId()

getReadMetadata

public ReadMetadata getReadMetadata()

getHeaderBroadcast

public org.apache.spark.broadcast.Broadcast<htsjdk.samtools.SAMFileHeader> getHeaderBroadcast()

getCnvCallsBroadcast

public org.apache.spark.broadcast.Broadcast<SVIntervalTree<htsjdk.variant.variantcontext.VariantContext>> getCnvCallsBroadcast()

getEvidenceTargetLinks

public PairedStrandedIntervalTree<EvidenceTargetLink> getEvidenceTargetLinks()

getAssembledIntervals

public java.util.List<SVInterval> getAssembledIntervals()