Package picard.analysis.directed
Class TargetedPcrMetricsCollector
java.lang.Object
picard.metrics.MultiLevelCollector<BEAN,HKEY,htsjdk.samtools.SAMRecord>
picard.metrics.SAMRecordMultiLevelCollector<METRIC_TYPE,Integer>
picard.analysis.directed.TargetMetricsCollector<TargetedPcrMetrics>
picard.analysis.directed.TargetedPcrMetricsCollector
Calculates HS metrics for a given SAM or BAM file. Requires the input of a list of
target intervals and a list of bait intervals. Can be invoked either on an entire
iterator of SAMRecords or be passed SAMRecords one at a time.
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Nested Class Summary
Nested classes/interfaces inherited from class picard.analysis.directed.TargetMetricsCollector
TargetMetricsCollector.Coverage, TargetMetricsCollector.PerUnitTargetMetricCollector
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Field Summary
Fields inherited from class picard.analysis.directed.TargetMetricsCollector
NEAR_PROBE_DISTANCE_DEFAULT
Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
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Constructor Summary
ConstructorsConstructorDescriptionTargetedPcrMetricsCollector
(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, boolean includeIndels, 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) -
Method Summary
Methods inherited from class picard.analysis.directed.TargetMetricsCollector
getBaseQualityHistogram, getDepthHistogram, getNearProbeDistance, getNumBasesPassingMinimumBaseQuality, makeAllReadCollector, makeChildCollector, reflectiveCopy, setNearProbeDistance, setNoSideEffects
Methods inherited from class picard.metrics.SAMRecordMultiLevelCollector
makeArg
Methods inherited from class picard.metrics.MultiLevelCollector
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
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Constructor Details
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TargetedPcrMetricsCollector
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) -
TargetedPcrMetricsCollector
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, boolean includeIndels, int coverageCap, int sampleSize)
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Method Details
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convertMetric
- Specified by:
convertMetric
in classTargetMetricsCollector<TargetedPcrMetrics>
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