Package picard.illumina.quality
Class CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
- Enclosing class:
- CollectHiSeqXPfFailMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
extends htsjdk.samtools.metrics.MetricBase
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
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Field Summary
FieldsModifier and TypeFieldDescriptionThe classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)int
The number of Ns found in this readint
The number of Quality scores greater than 2 found in this readThe Tile that is described by this metricint
The X coordinate of the read within the tileint
The Y coordinate of the read within the tile -
Constructor Summary
ConstructorsConstructorDescriptionThis ctor is necessary for when reading metrics from filePFFailDetailedMetric
(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
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Field Details
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TILE
The Tile that is described by this metric -
X
public int XThe X coordinate of the read within the tile -
Y
public int YThe Y coordinate of the read within the tile -
NUM_N
public int NUM_NThe number of Ns found in this read -
NUM_Q_GT_TWO
public int NUM_Q_GT_TWOThe number of Quality scores greater than 2 found in this read -
CLASSIFICATION
The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)
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Constructor Details
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PFFailDetailedMetric
public PFFailDetailedMetric(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
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