org.broadinstitute.hellbender.engine

Class AlignmentContext

java.lang.Object

org.broadinstitute.hellbender.engine.AlignmentContext

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, HasGenomeLocation

public final class AlignmentContext
extends java.lang.Object
implements htsjdk.samtools.util.Locatable, HasGenomeLocation

Bundles together a pileup and a location.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AlignmentContext.ReadOrientation

Constructor Summary

Constructors

Constructor and Description
AlignmentContext(htsjdk.samtools.util.Locatable loc, ReadPileup basePileup)
AlignmentContext(htsjdk.samtools.util.Locatable loc, ReadPileup basePileup, boolean hasPileupBeenDownsampled)

Method Summary

Modifier and Type	Method and Description
ReadPileup	getBasePileup()
java.lang.String	getContig()
int	getEnd()
htsjdk.samtools.util.Locatable	getLocation()
long	getPosition()
int	getStart()
boolean	hasPileupBeenDownsampled() Returns true if any reads have been filtered out of the pileup due to excess DoC.
int	size() How many reads cover this locus?
static java.util.Map<java.lang.String,AlignmentContext>	splitContextBySampleName(ReadPileup pileup, htsjdk.samtools.SAMFileHeader header)
java.util.Map<java.lang.String,AlignmentContext>	splitContextBySampleName(htsjdk.samtools.SAMFileHeader header)
java.util.Map<java.lang.String,AlignmentContext>	splitContextBySampleName(java.lang.String assumedSingleSample, htsjdk.samtools.SAMFileHeader header) Splits the given AlignmentContext into a StratifiedAlignmentContext per sample, but referenced by sample name instead of sample object.
AlignmentContext	stratify(AlignmentContext.ReadOrientation type) Returns a potentially derived subcontext containing only forward, reverse, or in fact all reads in alignment context context.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Constructor Detail

AlignmentContext

public AlignmentContext(htsjdk.samtools.util.Locatable loc,
                        ReadPileup basePileup)

AlignmentContext

public AlignmentContext(htsjdk.samtools.util.Locatable loc,
                        ReadPileup basePileup,
                        boolean hasPileupBeenDownsampled)

Method Detail

size

public int size()

How many reads cover this locus?

Returns:

getContig

public java.lang.String getContig()

Specified by:

getContig in interface htsjdk.samtools.util.Locatable

getStart

public int getStart()

Specified by:

getStart in interface htsjdk.samtools.util.Locatable

getEnd

public int getEnd()

Specified by:

getEnd in interface htsjdk.samtools.util.Locatable

getPosition

public long getPosition()

getLocation

public htsjdk.samtools.util.Locatable getLocation()

Specified by:

getLocation in interface HasGenomeLocation

hasPileupBeenDownsampled

public boolean hasPileupBeenDownsampled()

Returns true if any reads have been filtered out of the pileup due to excess DoC.

Returns:

True if reads have been filtered out. False otherwise.

getBasePileup

public ReadPileup getBasePileup()

stratify

public AlignmentContext stratify(AlignmentContext.ReadOrientation type)

Returns a potentially derived subcontext containing only forward, reverse, or in fact all reads in alignment context context.

splitContextBySampleName

public java.util.Map<java.lang.String,AlignmentContext> splitContextBySampleName(htsjdk.samtools.SAMFileHeader header)

splitContextBySampleName

public java.util.Map<java.lang.String,AlignmentContext> splitContextBySampleName(java.lang.String assumedSingleSample,
                                                                                 htsjdk.samtools.SAMFileHeader header)

Splits the given AlignmentContext into a StratifiedAlignmentContext per sample, but referenced by sample name instead of sample object.

Parameters:

assumedSingleSample - If non-null, assume this is the only sample in our pileup and return immediately. If null, get the list of samples from the provided header and do the work of splitting by sample.

Returns:

a Map of sample name to StratifiedAlignmentContext; samples without coverage are not included

splitContextBySampleName

public static java.util.Map<java.lang.String,AlignmentContext> splitContextBySampleName(ReadPileup pileup,
                                                                                        htsjdk.samtools.SAMFileHeader header)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object