public class InsertSizeMetricsCollector extends MultiLevelCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>
Modifier and Type | Class and Description |
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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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UNKNOWN
Constructor and Description |
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InsertSizeMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
double minimumPct,
java.lang.Integer histogramWidth,
double deviations,
boolean includeDuplicates) |
Modifier and Type | Method and Description |
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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 record
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protected picard.analysis.directed.InsertSizeCollectorArgs |
makeArg(htsjdk.samtools.SAMRecord samRecord,
htsjdk.samtools.reference.ReferenceSequence refSeq) |
protected PerUnitMetricCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs> |
makeChildCollector(java.lang.String sample,
java.lang.String library,
java.lang.String readGroup)
Make an InsertSizeCollector with the given arguments
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addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
public InsertSizeMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, double minimumPct, java.lang.Integer histogramWidth, double deviations, boolean includeDuplicates)
protected picard.analysis.directed.InsertSizeCollectorArgs makeArg(htsjdk.samtools.SAMRecord samRecord, htsjdk.samtools.reference.ReferenceSequence refSeq)
makeArg
in class MultiLevelCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>
protected PerUnitMetricCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs> makeChildCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup)
makeChildCollector
in class MultiLevelCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>
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 collectorpublic void acceptRecord(htsjdk.samtools.SAMRecord record, htsjdk.samtools.reference.ReferenceSequence refSeq)
MultiLevelCollector
acceptRecord
in class MultiLevelCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>