picard.analysis.directed

Class HsMetricCollector

java.lang.Object

picard.metrics.MultiLevelCollector<BEAN,HKEY,htsjdk.samtools.SAMRecord>

picard.metrics.SAMRecordMultiLevelCollector<METRIC_TYPE,java.lang.Integer>

picard.analysis.directed.TargetMetricsCollector<HsMetrics>

picard.analysis.directed.HsMetricCollector

public class HsMetricCollector
extends TargetMetricsCollector<HsMetrics>

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.

Nested Class Summary

Nested classes/interfaces inherited from class picard.analysis.directed.TargetMetricsCollector

TargetMetricsCollector.Coverage, TargetMetricsCollector.PerUnitTargetMetricCollector

Field Summary

Fields inherited from class picard.analysis.directed.TargetMetricsCollector

NEAR_PROBE_DISTANCE_DEFAULT

Fields inherited from class picard.metrics.MultiLevelCollector

UNKNOWN

Constructor Summary

Constructors

Constructor and Description
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, boolean includeIndels, 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)

Method Summary

Modifier and Type	Method and Description
HsMetrics	convertMetric(TargetMetrics targetMetrics)

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HsMetricCollector

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)

HsMetricCollector

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,
                         boolean includeIndels,
                         int coverageCap,
                         int sampleSize)

Method Detail

convertMetric

public HsMetrics convertMetric(TargetMetrics targetMetrics)

Specified by:

convertMetric in class TargetMetricsCollector<HsMetrics>