public abstract static class BreakpointEvidence.DiscordantReadPairEvidence extends BreakpointEvidence.ReadEvidence
BreakpointEvidence.ReadEvidence.Serializer
BreakpointEvidence.DiscordantReadPairEvidence, BreakpointEvidence.ExternalEvidence, BreakpointEvidence.InterContigPair, BreakpointEvidence.LargeIndel, BreakpointEvidence.MateUnmapped, BreakpointEvidence.OutiesPair, BreakpointEvidence.ReadEvidence, BreakpointEvidence.SameStrandPair, BreakpointEvidence.SplitRead, BreakpointEvidence.TemplateSizeAnomaly, BreakpointEvidence.WeirdTemplateSize
Modifier and Type | Field and Description |
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static int |
MATE_ALIGNMENT_LENGTH_UNCERTAINTY |
protected SVInterval |
target |
protected boolean |
targetForwardStrand |
protected int |
targetQuality |
Constructor and Description |
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DiscordantReadPairEvidence(GATKRead read,
ReadMetadata metadata,
int weight) |
DiscordantReadPairEvidence(com.esotericsoftware.kryo.Kryo kryo,
com.esotericsoftware.kryo.io.Input input) |
Modifier and Type | Method and Description |
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java.util.List<StrandedInterval> |
getDistalTargets(ReadMetadata readMetadata,
int minEvidenceMapq)
In the case of a discordant read pair, the distal target interval is a StrandedInterval where the interval
location is the possible breakpoint interval given by the inferred rest-of-fragment interval for the mate read
(ie the region that would contain the mate's mated read if its fragment size had been drawn from the non-outlier
fragment size distribution), and the strand can be easily computed as the strand of the reference the mate
mapped to.
|
protected boolean |
getMateForwardStrand(GATKRead read) |
protected SVInterval |
getMateTargetInterval(GATKRead read,
ReadMetadata metadata)
Finds the coordinates implicated by the read's mate as being part of the breakpoint, ie.
|
boolean |
hasDistalTargets(ReadMetadata readMetadata,
int minEvidenceMapQ)
Returns true if this piece of evidence specifies a possible distal target for the breakpoint.
|
protected void |
serialize(com.esotericsoftware.kryo.Kryo kryo,
com.esotericsoftware.kryo.io.Output output) |
getCigarString, getFragmentOrdinal, getMappingQuality, getTemplateName, getTemplateSize, isEvidenceUpstreamOfBreakpoint, stringRep, toString
equalFields, getLocation, getWeight, isValidated, setValidated
protected final SVInterval target
protected final boolean targetForwardStrand
protected final int targetQuality
public static final int MATE_ALIGNMENT_LENGTH_UNCERTAINTY
public DiscordantReadPairEvidence(GATKRead read, ReadMetadata metadata, int weight)
public DiscordantReadPairEvidence(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Input input)
protected void serialize(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Output output)
serialize
in class BreakpointEvidence.ReadEvidence
public boolean hasDistalTargets(ReadMetadata readMetadata, int minEvidenceMapQ)
BreakpointEvidence
hasDistalTargets
in class BreakpointEvidence
readMetadata
- Read metadata for the libraryminEvidenceMapQ
- The minimum mapping quality threshold (inclusive) for which a target (mate or SA mapping) should be createdpublic java.util.List<StrandedInterval> getDistalTargets(ReadMetadata readMetadata, int minEvidenceMapq)
getDistalTargets
in class BreakpointEvidence
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 targetprotected SVInterval getMateTargetInterval(GATKRead read, ReadMetadata metadata)
protected boolean getMateForwardStrand(GATKRead read)