picard.analysis

Class GcBiasDetailMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.metrics.MultilevelMetrics

picard.analysis.GcBiasDetailMetrics

public class GcBiasDetailMetrics
extends MultilevelMetrics

Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	ACCUMULATION_LEVEL
double	ERROR_BAR_WIDTH The radius of error bars in this bin based on the number of observations made.
int	GC The G+C content of the reference sequence represented by this bin.
int	MEAN_BASE_QUALITY The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
double	NORMALIZED_COVERAGE The ration of "coverage" in this GC bin vs.
long	READ_STARTS The number of reads whose start position is at the start of a window of this GC.
int	WINDOWS The number of windows on the reference genome that have this G+C content.

Fields inherited from class picard.metrics.MultilevelMetrics

LIBRARY, READ_GROUP, SAMPLE

Constructor Summary

Constructors

Constructor and Description
GcBiasDetailMetrics()

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

ACCUMULATION_LEVEL

public java.lang.String ACCUMULATION_LEVEL

GC

public int GC

The G+C content of the reference sequence represented by this bin. Values are from 0% to 100%

WINDOWS

public int WINDOWS

The number of windows on the reference genome that have this G+C content.

READ_STARTS

public long READ_STARTS

The number of reads whose start position is at the start of a window of this GC.

MEAN_BASE_QUALITY

public int MEAN_BASE_QUALITY

The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.

NORMALIZED_COVERAGE

public double NORMALIZED_COVERAGE

The ration of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average).

ERROR_BAR_WIDTH

public double ERROR_BAR_WIDTH

The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85.

Constructor Detail

GcBiasDetailMetrics

public GcBiasDetailMetrics()