Package picard.illumina
Class IlluminaPhasingMetrics
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- htsjdk.samtools.metrics.MetricBase
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- picard.illumina.IlluminaPhasingMetrics
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@DocumentedFeature(groupName="Metrics", summary="Metrics") public class IlluminaPhasingMetrics extends htsjdk.samtools.metrics.MetricBase
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis. Phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle. For each lane/template read # (i.e. FIRST, SECOND) combination we will store the median values of both the phasing and prephasing values for every tile in that lane/template read pair.
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Field Summary
Fields Modifier and Type Field Description long
LANE
Illumina flowcell lane numberdouble
PHASING_APPLIED
Median phasing value across all tiles in a lane, applied to the first and second template readsdouble
PREPHASING_APPLIED
Median pre-phasing value across all tiles in a lane, applied to the first and second template readsString
TYPE_NAME
Defines an Illumina template read number (first or second)
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Constructor Summary
Constructors Constructor Description IlluminaPhasingMetrics()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static String
getExtension()
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.static Collection<IlluminaPhasingMetrics>
getPhasingMetricsForTiles(long lane, Collection<Tile> tilesForLane, boolean usePercentage)
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
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Field Detail
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LANE
public long LANE
Illumina flowcell lane number
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TYPE_NAME
public String TYPE_NAME
Defines an Illumina template read number (first or second)
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PHASING_APPLIED
public double PHASING_APPLIED
Median phasing value across all tiles in a lane, applied to the first and second template reads
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PREPHASING_APPLIED
public double PREPHASING_APPLIED
Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
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Method Detail
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getPhasingMetricsForTiles
public static Collection<IlluminaPhasingMetrics> getPhasingMetricsForTiles(long lane, Collection<Tile> tilesForLane, boolean usePercentage)
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
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getExtension
public static String getExtension()
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
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