Package | Description |
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picard.analysis | |
picard.analysis.directed | |
picard.metrics |
Modifier and Type | Field and Description |
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Set<MetricAccumulationLevel> |
CollectGcBiasMetrics.METRIC_ACCUMULATION_LEVEL |
Set<MetricAccumulationLevel> |
CollectRrbsMetrics.METRIC_ACCUMULATION_LEVEL |
Modifier and Type | Method and Description |
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static MetricAccumulationLevel |
MetricAccumulationLevel.valueOf(String name)
Returns the enum constant of this type with the specified name.
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static MetricAccumulationLevel[] |
MetricAccumulationLevel.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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Constructor and Description |
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AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
boolean doRefMetrics,
List<String> adapterSequence,
int maxInsertSize,
boolean isBisulfiteSequenced) |
RrbsMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
int cQualityThreshold,
int nextBaseQualityThreshold,
int minReadLength,
double maxMismatchRate) |
Modifier and Type | Field and Description |
---|---|
Set<MetricAccumulationLevel> |
CollectTargetedMetrics.METRIC_ACCUMULATION_LEVEL |
Modifier and Type | Method and Description |
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protected HsMetricCollector |
CalculateHsMetrics.makeCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName) |
protected abstract COLLECTOR |
CollectTargetedMetrics.makeCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName)
A factory method for the TargetMetricsCollector to use this time.
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protected TargetedPcrMetricsCollector |
CollectTargetedPcrMetrics.makeCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName) |
Constructor and Description |
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GcBiasMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
Map<String,byte[]> gcByRef,
int[] windowsByGc,
List<SAMReadGroupRecord> samRgRecords,
int windowSize,
boolean bisulfite) |
HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName) |
InsertSizeMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
double minimumPct,
Integer HistogramWidth,
double deviations) |
RnaSeqMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
Long ribosomalBasesInitialValue,
OverlapDetector<Gene> geneOverlapDetector,
OverlapDetector<Interval> ribosomalSequenceOverlapDetector,
HashSet<Integer> ignoredSequenceIndices,
int minimumLength,
RnaSeqMetricsCollector.StrandSpecificity strandSpecificity,
double rrnaFragmentPercentage,
boolean collectCoverageStatistics) |
TargetedPcrMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName) |
TargetMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName) |
Modifier and Type | Method and Description |
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protected void |
MultiLevelCollector.setup(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords)
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
|