picard.illumina.quality

Class CollectHiSeqXPfFailMetrics.PFFailDetailedMetric

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric

Enclosing class:

CollectHiSeqXPfFailMetrics

public static class CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
extends htsjdk.samtools.metrics.MetricBase

a metric class for describing FP failing reads from an Illumina HiSeqX lane *

Field Summary

Fields

Modifier and Type	Field and Description
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason	CLASSIFICATION The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)
int	NUM_N
int	NUM_Q_GT_TWO
java.lang.Integer	TILE
int	X
int	Y

Constructor Summary

Constructors

Constructor and Description
PFFailDetailedMetric() This ctor is necessary for when reading metrics from file
PFFailDetailedMetric(java.lang.Integer TILE, int x, int y, int NUM_N, int NUM_Q_GT_TWO, CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason CLASSIFICATION)

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

TILE

public java.lang.Integer TILE

X

public int X

Y

public int Y

NUM_N

public int NUM_N

NUM_Q_GT_TWO

public int NUM_Q_GT_TWO

CLASSIFICATION

public CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason CLASSIFICATION

The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)

Constructor Detail

PFFailDetailedMetric

public PFFailDetailedMetric(java.lang.Integer TILE,
                            int x,
                            int y,
                            int NUM_N,
                            int NUM_Q_GT_TWO,
                            CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason CLASSIFICATION)

PFFailDetailedMetric

public PFFailDetailedMetric()

This ctor is necessary for when reading metrics from file