Uses of Class
picard.analysis.MetricAccumulationLevel

Packages that use MetricAccumulationLevel

Package	Description
picard.analysis
picard.analysis.directed
picard.metrics

Uses of MetricAccumulationLevel in picard.analysis

Fields in picard.analysis with type parameters of type MetricAccumulationLevel

Modifier and Type	Field and Description
java.util.Set<MetricAccumulationLevel>	CollectAlignmentSummaryMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectGcBiasMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectInsertSizeMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectMultipleMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectRnaSeqMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectRrbsMetrics.METRIC_ACCUMULATION_LEVEL

Methods in picard.analysis that return MetricAccumulationLevel

Modifier and Type	Method and Description
static MetricAccumulationLevel	MetricAccumulationLevel.valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static MetricAccumulationLevel[]	MetricAccumulationLevel.values() Returns an array containing the constants of this enum type, in the order they are declared.

Method parameters in picard.analysis with type arguments of type MetricAccumulationLevel

Modifier and Type	Method and Description
SinglePassSamProgram	CollectMultipleMetrics.ProgramInterface.makeInstance(java.lang.String outbase, java.lang.String outext, java.io.File input, java.io.File reference, java.util.Set<MetricAccumulationLevel> metricAccumulationLevel, java.io.File dbSnp, java.io.File intervals)

Constructor parameters in picard.analysis with type arguments of type MetricAccumulationLevel

Constructor and Description
AlignmentSummaryMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, boolean doRefMetrics, java.util.List<java.lang.String> adapterSequence, int maxInsertSize, java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, boolean isBisulfiteSequenced)
GcBiasMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite)
RrbsMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int cQualityThreshold, int nextBaseQualityThreshold, int minReadLength, double maxMismatchRate)

Uses of MetricAccumulationLevel in picard.analysis.directed

Fields in picard.analysis.directed with type parameters of type MetricAccumulationLevel

Modifier and Type	Field and Description
java.util.Set<MetricAccumulationLevel>	CollectTargetedMetrics.METRIC_ACCUMULATION_LEVEL

Method parameters in picard.analysis.directed with type arguments of type MetricAccumulationLevel

Modifier and Type	Method and Description
protected HsMetricCollector	CollectHsMetrics.makeCollector(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)
protected abstract COLLECTOR	CollectTargetedMetrics.makeCollector(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) A factory method for the TargetMetricsCollector to use this time.
protected TargetedPcrMetricsCollector	CollectTargetedPcrMetrics.makeCollector(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)

Constructor parameters in picard.analysis.directed with type arguments of type MetricAccumulationLevel

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, 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)
InsertSizeMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, double minimumPct, java.lang.Integer histogramWidth, double deviations, boolean includeDuplicates)
RnaSeqMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, java.lang.Long ribosomalBasesInitialValue, htsjdk.samtools.util.OverlapDetector<Gene> geneOverlapDetector, htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> ribosomalSequenceOverlapDetector, java.util.HashSet<java.lang.Integer> ignoredSequenceIndices, int minimumLength, RnaSeqMetricsCollector.StrandSpecificity strandSpecificity, double rrnaFragmentPercentage, boolean collectCoverageStatistics)
TargetedPcrMetricsCollector(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)
TargetedPcrMetricsCollector(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)
TargetMetricsCollector(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)
TargetMetricsCollector(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)

Uses of MetricAccumulationLevel in picard.metrics

Method parameters in picard.metrics with type arguments of type MetricAccumulationLevel

Modifier and Type	Method and Description
protected void	MultiLevelCollector.setup(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords) Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor