org.broadinstitute.hellbender.tools.sv

Class LocusDepth

java.lang.Object

org.broadinstitute.hellbender.tools.sv.LocusDepth

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, htsjdk.tribble.Feature

public final class LocusDepth
extends java.lang.Object
implements htsjdk.tribble.Feature

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BCI_VERSION

Constructor Summary

Constructors

Constructor and Description
LocusDepth(java.io.DataInputStream dis, htsjdk.samtools.SAMSequenceDictionary dict)
LocusDepth(htsjdk.samtools.util.Locatable loc, byte refCall)
LocusDepth(java.lang.String contig, int position, byte refCall, int aDepth, int cDepth, int gDepth, int tDepth)

Method Summary

Modifier and Type	Method and Description
int	getADepth()
int	getCDepth()
java.lang.String	getContig()
int	getEnd()
int	getGDepth()
char	getRefCall()
int	getStart()
int	getTDepth()
void	observe(int idx)
java.lang.String	toString()
void	write(java.io.DataOutputStream dos, htsjdk.samtools.SAMSequenceDictionary dict)

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.tribble.Feature

getChr

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Field Detail

BCI_VERSION

public static final java.lang.String BCI_VERSION

See Also:

Constant Field Values

Constructor Detail

LocusDepth

public LocusDepth(htsjdk.samtools.util.Locatable loc,
                  byte refCall)

LocusDepth

public LocusDepth(java.lang.String contig,
                  int position,
                  byte refCall,
                  int aDepth,
                  int cDepth,
                  int gDepth,
                  int tDepth)

LocusDepth

public LocusDepth(java.io.DataInputStream dis,
                  htsjdk.samtools.SAMSequenceDictionary dict)
           throws java.io.IOException

Throws:

java.io.IOException

Method Detail

observe

public void observe(int idx)

getContig

public java.lang.String getContig()

Specified by:

getContig in interface htsjdk.samtools.util.Locatable

getEnd

public int getEnd()

Specified by:

getEnd in interface htsjdk.samtools.util.Locatable

getStart

public int getStart()

Specified by:

getStart in interface htsjdk.samtools.util.Locatable

getRefCall

public char getRefCall()

getADepth

public int getADepth()

getCDepth

public int getCDepth()

getGDepth

public int getGDepth()

getTDepth

public int getTDepth()

write

public void write(java.io.DataOutputStream dos,
                  htsjdk.samtools.SAMSequenceDictionary dict)
           throws java.io.IOException

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object