Package picard.analysis
Class GcBiasDetailMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.GcBiasDetailMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
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.
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Field Summary
FieldsModifier and TypeFieldDescriptiondouble
The radius of error bars in this bin based on the number of observations made.int
The G+C content of the reference sequence represented by this bin.int
The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.double
The ratio of "coverage" in this GC bin vs.long
The number of reads whose start position is at the start of a window of this GC.This option is used to mark including or excluding duplicates.int
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
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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ACCUMULATION_LEVEL
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READS_USED
This option is used to mark including or excluding duplicates. -
GC
public int GCThe G+C content of the reference sequence represented by this bin. Values are from 0% to 100% -
WINDOWS
public int WINDOWSThe number of windows on the reference genome that have this G+C content. -
READ_STARTS
public long READ_STARTSThe number of reads whose start position is at the start of a window of this GC. -
MEAN_BASE_QUALITY
public int MEAN_BASE_QUALITYThe 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_COVERAGEThe ratio 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_WIDTHThe 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.
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Constructor Details
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GcBiasDetailMetrics
public GcBiasDetailMetrics()
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