Package picard.illumina.quality
Class CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
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- htsjdk.samtools.metrics.MetricBase
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- picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
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- 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
Fields Modifier and Type Field 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
The number of Ns found in this readint
NUM_Q_GT_TWO
The number of Quality scores greater than 2 found in this readInteger
TILE
The Tile that is described by this metricint
X
The X coordinate of the read within the tileint
Y
The Y coordinate of the read within the tile
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Constructor Summary
Constructors Constructor Description PFFailDetailedMetric()
This 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)
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Field Detail
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TILE
public Integer TILE
The Tile that is described by this metric
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X
public int X
The X coordinate of the read within the tile
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Y
public int Y
The Y coordinate of the read within the tile
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NUM_N
public int NUM_N
The number of Ns found in this read
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NUM_Q_GT_TWO
public int NUM_Q_GT_TWO
The number of Quality scores greater than 2 found in this read
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CLASSIFICATION
public CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason CLASSIFICATION
The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)
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Constructor Detail
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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)
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PFFailDetailedMetric
public PFFailDetailedMetric()
This ctor is necessary for when reading metrics from file
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