Package picard.analysis.directed
Class InsertSizeMetricsCollector
- java.lang.Object
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- picard.metrics.MultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
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- picard.analysis.directed.InsertSizeMetricsCollector
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public class InsertSizeMetricsCollector extends MultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
Collects InsertSizeMetrics on the specified accumulationLevels using
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
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Field Summary
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Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
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Constructor Summary
Constructors Constructor Description InsertSizeMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, double minimumPct, Integer histogramWidth, double deviations, boolean includeDuplicates)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
acceptRecord(htsjdk.samtools.SAMRecord record, htsjdk.samtools.reference.ReferenceSequence refSeq)
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this recordprotected picard.analysis.directed.InsertSizeCollectorArgs
makeArg(htsjdk.samtools.SAMRecord samRecord, htsjdk.samtools.reference.ReferenceSequence refSeq)
protected PerUnitMetricCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
makeChildCollector(String sample, String library, String readGroup)
Make an InsertSizeCollector with the given arguments-
Methods inherited from class picard.metrics.MultiLevelCollector
addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
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Constructor Detail
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InsertSizeMetricsCollector
public InsertSizeMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, double minimumPct, Integer histogramWidth, double deviations, boolean includeDuplicates)
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Method Detail
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makeArg
protected picard.analysis.directed.InsertSizeCollectorArgs makeArg(htsjdk.samtools.SAMRecord samRecord, htsjdk.samtools.reference.ReferenceSequence refSeq)
- Specified by:
makeArg
in classMultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
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makeChildCollector
protected PerUnitMetricCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs> makeChildCollector(String sample, String library, String readGroup)
Make an InsertSizeCollector with the given arguments- Specified by:
makeChildCollector
in classMultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
- Parameters:
sample
- If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collectorlibrary
- If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collectorreadGroup
- If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector- Returns:
- A PerUnitMetricCollector parameterized by the given arguments
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acceptRecord
public void acceptRecord(htsjdk.samtools.SAMRecord record, htsjdk.samtools.reference.ReferenceSequence refSeq)
Description copied from class:MultiLevelCollector
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record- Overrides:
acceptRecord
in classMultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
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