Package picard.illumina
Class IlluminaBasecallingMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.illumina.IlluminaBasecallingMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class IlluminaBasecallingMetrics
extends htsjdk.samtools.metrics.MetricBase
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis. Averages
and means are taken over all tiles.
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Field Summary
FieldsModifier and TypeFieldDescriptionThe lane for which the metrics were calculated.double
The mean number of clusters per tile.double
The mean percentage of pf clusters per tile.double
The mean number of pf clusters per tile.The barcode name for which the metrics were calculated.The barcode sequence for which the metrics were calculated.long
The total number of passing-filter bases assigned to the index.long
The total number of PF clusters assigned to the index.long
The total number of passing-filter reads assigned to the index.double
The standard deviation of clusters per tile.double
The standard deviation in percentage of pf clusters per tile.double
The standard deviation in number of pf clusters per tile.long
The total number of bases assigned to the index.long
The total number of clusters assigned to the index.long
The total number of reads assigned to the index. -
Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode
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Field Details
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LANE
The lane for which the metrics were calculated. -
MOLECULAR_BARCODE_SEQUENCE_1
The barcode sequence for which the metrics were calculated. -
MOLECULAR_BARCODE_NAME
The barcode name for which the metrics were calculated. -
TOTAL_BASES
public long TOTAL_BASESThe total number of bases assigned to the index. -
PF_BASES
public long PF_BASESThe total number of passing-filter bases assigned to the index. -
TOTAL_READS
public long TOTAL_READSThe total number of reads assigned to the index. -
PF_READS
public long PF_READSThe total number of passing-filter reads assigned to the index. -
TOTAL_CLUSTERS
public long TOTAL_CLUSTERSThe total number of clusters assigned to the index. -
PF_CLUSTERS
public long PF_CLUSTERSThe total number of PF clusters assigned to the index. -
MEAN_CLUSTERS_PER_TILE
public double MEAN_CLUSTERS_PER_TILEThe mean number of clusters per tile. -
SD_CLUSTERS_PER_TILE
public double SD_CLUSTERS_PER_TILEThe standard deviation of clusters per tile. -
MEAN_PCT_PF_CLUSTERS_PER_TILE
public double MEAN_PCT_PF_CLUSTERS_PER_TILEThe mean percentage of pf clusters per tile. -
SD_PCT_PF_CLUSTERS_PER_TILE
public double SD_PCT_PF_CLUSTERS_PER_TILEThe standard deviation in percentage of pf clusters per tile. -
MEAN_PF_CLUSTERS_PER_TILE
public double MEAN_PF_CLUSTERS_PER_TILEThe mean number of pf clusters per tile. -
SD_PF_CLUSTERS_PER_TILE
public double SD_PF_CLUSTERS_PER_TILEThe standard deviation in number of pf clusters per tile.
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Constructor Details
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IlluminaBasecallingMetrics
public IlluminaBasecallingMetrics()
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Method Details
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toString
- Overrides:
toString
in classhtsjdk.samtools.metrics.MetricBase
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