picard.analysis.directed

Class TargetMetricsCollector.Coverage

java.lang.Object

picard.analysis.directed.TargetMetricsCollector.Coverage

Enclosing class:

TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>

public static class TargetMetricsCollector.Coverage
extends java.lang.Object

A simple class that is used to store the coverage information about an interval.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
long	readCount

Constructor Summary

Constructors

Constructor and Description
Coverage(htsjdk.samtools.util.Interval i, int padding) Constructs a new coverage object for the provided mapping with the desired padding either side.

Method Summary

Modifier and Type	Method and Description
void	addBase(int offset) Adds a single point of depth at the desired offset into the coverage array.
int[]	getDepths() Gets the coverage depths as an array of ints.
int	getTotal()
boolean	hasCoverage() Returns true if any base in the range has coverage of > 0
void	incrementReadCount() Increments the # of reads mapping to this target.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

readCount

public long readCount

Constructor Detail

Coverage

public Coverage(htsjdk.samtools.util.Interval i,
                int padding)

Constructs a new coverage object for the provided mapping with the desired padding either side.

Method Detail

addBase

public void addBase(int offset)

Adds a single point of depth at the desired offset into the coverage array.

incrementReadCount

public void incrementReadCount()

Increments the # of reads mapping to this target.

hasCoverage

public boolean hasCoverage()

Returns true if any base in the range has coverage of > 0

getDepths

public int[] getDepths()

Gets the coverage depths as an array of ints.

getTotal

public int getTotal()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object