org.broadinstitute.hellbender.tools.spark.sv.evidence

Class BreakpointEvidence.TemplateSizeAnomaly

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence

org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly

Enclosing class:

BreakpointEvidence

public static final class BreakpointEvidence.TemplateSizeAnomaly
extends BreakpointEvidence

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BreakpointEvidence.TemplateSizeAnomaly.Serializer

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence

BreakpointEvidence.DiscordantReadPairEvidence, BreakpointEvidence.ExternalEvidence, BreakpointEvidence.InterContigPair, BreakpointEvidence.LargeIndel, BreakpointEvidence.MateUnmapped, BreakpointEvidence.OutiesPair, BreakpointEvidence.ReadEvidence, BreakpointEvidence.SameStrandPair, BreakpointEvidence.SplitRead, BreakpointEvidence.TemplateSizeAnomaly, BreakpointEvidence.WeirdTemplateSize

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	TemplateSizeAnomaly(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Input input)
	TemplateSizeAnomaly(SVInterval interval, int weight, int readCount)

Method Summary

Modifier and Type	Method and Description
protected void	serialize(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Output output)
java.lang.String	stringRep(ReadMetadata readMetadata, int minEvidenceMapq) Returns string representation of BreakpointEvidence in tab-separated form: Contig[begin:end] weight validated EvidenceType distal_targets distal_targets is a (; separated) list of string representations (.toString()) for each distal target it is empty if there are no distal targets Child classes may extend stringRep() by appending class-specific tab-separated info
java.lang.String	toString()

Methods inherited from class org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence

equalFields, getDistalTargets, getLocation, getWeight, hasDistalTargets, isEvidenceUpstreamOfBreakpoint, isValidated, setValidated

Methods inherited from class java.lang.Object

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

Constructor Detail

TemplateSizeAnomaly

public TemplateSizeAnomaly(SVInterval interval,
                           int weight,
                           int readCount)

TemplateSizeAnomaly

protected TemplateSizeAnomaly(com.esotericsoftware.kryo.Kryo kryo,
                              com.esotericsoftware.kryo.io.Input input)

Method Detail

serialize

protected void serialize(com.esotericsoftware.kryo.Kryo kryo,
                         com.esotericsoftware.kryo.io.Output output)

Overrides:

serialize in class BreakpointEvidence

toString

public java.lang.String toString()

Overrides:

toString in class BreakpointEvidence

stringRep

public java.lang.String stringRep(ReadMetadata readMetadata,
                                  int minEvidenceMapq)

Description copied from class: BreakpointEvidence

Returns string representation of BreakpointEvidence in tab-separated form: Contig[begin:end] weight validated EvidenceType distal_targets distal_targets is a (; separated) list of string representations (.toString()) for each distal target it is empty if there are no distal targets Child classes may extend stringRep() by appending class-specific tab-separated info

Overrides:

stringRep in class BreakpointEvidence