Package org.broadinstitute.hellbender.utils.read

Class Fragment

java.lang.Object

org.broadinstitute.hellbender.utils.read.Fragment

All Implemented Interfaces:

htsjdk.samtools.util.Locatable

public class Fragment
extends Object
implements htsjdk.samtools.util.Locatable

All available evidence coming from a single biological fragment. Either one read or a read pair.

Constructor Summary

Constructors

Constructor	Description
Fragment(org.apache.commons.lang3.tuple.Pair<GATKRead,GATKRead> pair)
Fragment(GATKRead read)

Method Summary

Modifier and Type	Method	Description
static Fragment	create(List<GATKRead> reads)
static Fragment	createAndAvoidFailure(List<GATKRead> reads)
String	getContig()
int	getEnd()
List<GATKRead>	getReads()
int	getStart()

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Constructor Details

Fragment

public Fragment(GATKRead read)

Fragment

public Fragment(org.apache.commons.lang3.tuple.Pair<GATKRead,GATKRead> pair)

Method Details

create

public static Fragment create(List<GATKRead> reads)

createAndAvoidFailure

public static Fragment createAndAvoidFailure(List<GATKRead> reads)

getReads

public List<GATKRead> getReads()

getContig

public 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