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

Class BreakpointEvidence

java.lang.Object

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

Direct Known Subclasses:

BreakpointEvidence.ExternalEvidence, BreakpointEvidence.ReadEvidence, BreakpointEvidence.TemplateSizeAnomaly

public class BreakpointEvidence
extends java.lang.Object

Various types of read anomalies that provide evidence of genomic breakpoints. There is a shallow hierarchy based on this class that classifies the anomaly as, for example, a split read, or a pair that has both reads on the same reference strand. Each BreakpointEvidence object of type ReadEvidence object comes from examining a single read, and describing its funkiness, if any, by instantiating one of the subclasses that addresses that type of funkiness. Instances of BreakpointEvidence that are not of subtype ReadEvidence consolidate information from one or more pieces of ReadEvidence into a single object.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BreakpointEvidence.DiscordantReadPairEvidence
static class	BreakpointEvidence.ExternalEvidence
static class	BreakpointEvidence.InterContigPair
static class	BreakpointEvidence.LargeIndel
static class	BreakpointEvidence.MateUnmapped
static class	BreakpointEvidence.OutiesPair
static class	BreakpointEvidence.ReadEvidence
static class	BreakpointEvidence.SameStrandPair
static class	BreakpointEvidence.Serializer
static class	BreakpointEvidence.SplitRead
static class	BreakpointEvidence.TemplateSizeAnomaly
static class	BreakpointEvidence.WeirdTemplateSize

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	BreakpointEvidence(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Input input)
	BreakpointEvidence(SVInterval location, int weight, boolean validated)

Method Summary

Modifier and Type	Method and Description
boolean	equalFields(BreakpointEvidence that)
java.util.List<StrandedInterval>	getDistalTargets(ReadMetadata readMetadata, int minEvidenceMapq) Returns the distal interval implicated as a candidate adjacency to the breakpoint by this piece of evidence.
SVInterval	getLocation()
int	getWeight()
boolean	hasDistalTargets(ReadMetadata readMetadata, int minEvidenceMapQ) Returns true if this piece of evidence specifies a possible distal target for the breakpoint.
java.lang.Boolean	isEvidenceUpstreamOfBreakpoint() If true: the evidence suggests a breakpoint at a reference location upstream of the interval's start coordinate If false: the evidence suggests a breakpoint downstream of the interval's end coordinate
boolean	isValidated()
protected void	serialize(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Output output)
void	setValidated(boolean validated)
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 java.lang.Object

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

Constructor Detail

BreakpointEvidence

public BreakpointEvidence(SVInterval location,
                          int weight,
                          boolean validated)

BreakpointEvidence

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

Method Detail

getLocation

public SVInterval getLocation()

getWeight

public int getWeight()

isValidated

public boolean isValidated()

setValidated

public void setValidated(boolean validated)

isEvidenceUpstreamOfBreakpoint

public java.lang.Boolean isEvidenceUpstreamOfBreakpoint()

If true: the evidence suggests a breakpoint at a reference location upstream of the interval's start coordinate If false: the evidence suggests a breakpoint downstream of the interval's end coordinate

hasDistalTargets

public boolean hasDistalTargets(ReadMetadata readMetadata,
                                int minEvidenceMapQ)

Returns true if this piece of evidence specifies a possible distal target for the breakpoint.

Parameters:

readMetadata - Read metadata for the library

minEvidenceMapQ - The minimum mapping quality threshold (inclusive) for which a target (mate or SA mapping) should be created

getDistalTargets

public java.util.List<StrandedInterval> getDistalTargets(ReadMetadata readMetadata,
                                                         int minEvidenceMapq)

Returns the distal interval implicated as a candidate adjacency to the breakpoint by this piece of evidence. For example, in the case of a discordant read pair, this would be the region adjacent to the mate of the current read. Returns null if the evidence does not specify or support a possible targeted region (for example, the case of an read with an unmapped mate). Strands of the intervals indicate whether the distal target intervals are upstream or downstream of their proposed breakpoints: true indicates that the breakpoint is upstream of the interval start position; false indicates that the breakpoint is downstream of the interval end position.

Parameters:

minEvidenceMapq - The minimum mapping quality (inclusive) of the target evidence; if the mapping quality is below this value the evidence is treated as not having a distal target

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

stringRep

public 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

equalFields

public boolean equalFields(BreakpointEvidence that)

serialize

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