public class TargetedPcrMetricsCollector extends TargetMetricsCollector<TargetedPcrMetrics>
TargetMetricsCollector.Coverage, TargetMetricsCollector.PerUnitTargetMetricCollector
NEAR_PROBE_DISTANCE_DEFAULT
UNKNOWN
Constructor and Description |
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TargetedPcrMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
File perBaseCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName,
int nearProbeDistance,
int minimumMappingQuality,
int minimumBaseQuality,
boolean clipOverlappingReads,
boolean noSideEffects,
int coverageCap,
int sampleSize) |
TargetedPcrMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
File perBaseCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName,
int nearProbeDistance,
int minimumMappingQuality,
int minimumBaseQuality,
boolean clipOverlappingReads,
int coverageCap,
int sampleSize) |
Modifier and Type | Method and Description |
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TargetedPcrMetrics |
convertMetric(picard.analysis.directed.TargetMetrics targetMetrics) |
getNearProbeDistance, getNumBasesPassingMinimumBaseQuality, makeAllReadCollector, makeChildCollector, reflectiveCopy, setNearProbeDistance, setNoSideEffects
makeArg
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
public TargetedPcrMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<SAMReadGroupRecord> samRgRecords, ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, IntervalList targetIntervals, IntervalList probeIntervals, String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, int coverageCap, int sampleSize)
public TargetedPcrMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<SAMReadGroupRecord> samRgRecords, ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, IntervalList targetIntervals, IntervalList probeIntervals, String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, boolean noSideEffects, int coverageCap, int sampleSize)
public TargetedPcrMetrics convertMetric(picard.analysis.directed.TargetMetrics targetMetrics)
convertMetric
in class TargetMetricsCollector<TargetedPcrMetrics>