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