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