picard.illumina

Class IlluminaPhasingMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.illumina.IlluminaPhasingMetrics

public class IlluminaPhasingMetrics
extends htsjdk.samtools.metrics.MetricBase

Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis. Phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle. For each lane/template read # (i.e. FIRST, SECOND) combination we will store the median values of both the phasing and prephasing values for every tile in that lane/template read pair.

Field Summary

Fields

Modifier and Type	Field and Description
long	LANE Illumina flowcell lane number
double	PHASING_APPLIED Median phasing value across all tiles in a lane, applied to the first and second template reads
double	PREPHASING_APPLIED Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
java.lang.String	TYPE_NAME Defines an Illumina template read number (first or second)

Constructor Summary

Constructors

Constructor and Description
IlluminaPhasingMetrics()

Method Summary

Modifier and Type	Method and Description
static java.lang.String	getExtension() This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
static java.util.Collection<IlluminaPhasingMetrics>	getPhasingMetricsForTiles(long lane, java.util.Collection<Tile> tilesForLane, boolean usePercentage) Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them

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

LANE

public long LANE

Illumina flowcell lane number

TYPE_NAME

public java.lang.String TYPE_NAME

Defines an Illumina template read number (first or second)

PHASING_APPLIED

public double PHASING_APPLIED

Median phasing value across all tiles in a lane, applied to the first and second template reads

PREPHASING_APPLIED

public double PREPHASING_APPLIED

Median pre-phasing value across all tiles in a lane, applied to the first and second template reads

Constructor Detail

IlluminaPhasingMetrics

public IlluminaPhasingMetrics()

Method Detail

getPhasingMetricsForTiles

public static java.util.Collection<IlluminaPhasingMetrics> getPhasingMetricsForTiles(long lane,
                                                                                     java.util.Collection<Tile> tilesForLane,
                                                                                     boolean usePercentage)

Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them

getExtension

public static java.lang.String getExtension()

This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.