Package picard.illumina
Class IlluminaPhasingMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.illumina.IlluminaPhasingMetrics
@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
FieldsModifier and TypeFieldDescriptionlong
Illumina flowcell lane numberdouble
Median phasing value across all tiles in a lane, applied to the first and second template readsdouble
Median pre-phasing value across all tiles in a lane, applied to the first and second template readsDefines an Illumina template read number (first or second) -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic String
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 invalid input: '&' prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for themMethods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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LANE
public long LANEIllumina flowcell lane number -
TYPE_NAME
Defines an Illumina template read number (first or second) -
PHASING_APPLIED
public double PHASING_APPLIEDMedian phasing value across all tiles in a lane, applied to the first and second template reads -
PREPHASING_APPLIED
public double PREPHASING_APPLIEDMedian pre-phasing value across all tiles in a lane, applied to the first and second template reads
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Constructor Details
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IlluminaPhasingMetrics
public IlluminaPhasingMetrics()
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Method Details
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getPhasingMetricsForTiles
public static Collection<IlluminaPhasingMetrics> getPhasingMetricsForTiles(long lane, Collection<Tile> tilesForLane, boolean usePercentage) Calculate the median phasing invalid input: '&' prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them -
getExtension
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
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