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. 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.

Author:

jgentry

Field Summary

Fields

Modifier and Type	Field and Description
long	LANE
double	PHASING_APPLIED
double	PREPHASING_APPLIED
java.lang.String	TYPE_NAME

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) 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

TYPE_NAME

public java.lang.String TYPE_NAME

PHASING_APPLIED

public double PHASING_APPLIED

PREPHASING_APPLIED

public double PREPHASING_APPLIED

Constructor Detail

IlluminaPhasingMetrics

public IlluminaPhasingMetrics()

Method Detail

getPhasingMetricsForTiles

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

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.