Package picard.illumina.quality
Class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
- Enclosing class:
- CollectHiSeqXPfFailMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
extends htsjdk.samtools.metrics.MetricBase
Metrics produced by the GetHiSeqXPFFailMetrics program. Used to diagnose lanes from HiSeqX
Sequencing, providing the number and fraction of each of the reasons that reads could have not passed PF.
Possible reasons are EMPTY (reads from empty wells with no template strand), POLYCLONAL (reads from wells that had more than one strand
cloned in them), MISALIGNED (reads from wells that are near the edge of the tile), UNKNOWN (reads that didn't pass PF but couldn't be diagnosed)
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Field Summary
FieldsModifier and TypeFieldDescriptiondouble
The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).double
The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).double
The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).double
The fraction of PF_READSdouble
The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).int
The number of non-PF reads in this tile that are deemed empty.int
The number of non-PF reads in this tile that are deemed "misaligned".int
The number of non-PF reads in this tile that are deemed multiclonal.int
The number of non-PF reads in this tile.int
The number of non-PF reads in this tile that have not been classified.int
The total number of reads examinedThe Tile that is described by this metric. -
Constructor Summary
ConstructorsConstructorDescriptionThis ctor is necessary for when reading metrics from filePFFailSummaryMetric
(String tile) -
Method Summary
Modifier and TypeMethodDescriptionvoid
void
Adds the non-calculated fields from the other metric to this one.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. Can be a string (like "All") to mean some marginal over tiles. * -
READS
public int READSThe total number of reads examined -
PF_FAIL_READS
public int PF_FAIL_READSThe number of non-PF reads in this tile. -
PCT_PF_FAIL_READS
public double PCT_PF_FAIL_READSThe fraction of PF_READS -
PF_FAIL_EMPTY
public int PF_FAIL_EMPTYThe number of non-PF reads in this tile that are deemed empty. -
PCT_PF_FAIL_EMPTY
public double PCT_PF_FAIL_EMPTYThe fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads). -
PF_FAIL_POLYCLONAL
public int PF_FAIL_POLYCLONALThe number of non-PF reads in this tile that are deemed multiclonal. -
PCT_PF_FAIL_POLYCLONAL
public double PCT_PF_FAIL_POLYCLONALThe fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads). -
PF_FAIL_MISALIGNED
public int PF_FAIL_MISALIGNEDThe number of non-PF reads in this tile that are deemed "misaligned". -
PCT_PF_FAIL_MISALIGNED
public double PCT_PF_FAIL_MISALIGNEDThe fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads). -
PF_FAIL_UNKNOWN
public int PF_FAIL_UNKNOWNThe number of non-PF reads in this tile that have not been classified. -
PCT_PF_FAIL_UNKNOWN
public double PCT_PF_FAIL_UNKNOWNThe fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
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Constructor Details
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PFFailSummaryMetric
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PFFailSummaryMetric
public PFFailSummaryMetric()This ctor is necessary for when reading metrics from file
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Method Details
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merge
Adds the non-calculated fields from the other metric to this one.- Parameters:
metric
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calculateDerivedFields
public void calculateDerivedFields()
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