picard.analysis.directed

Class InsertSizeMetricsCollector

java.lang.Object

picard.metrics.MultiLevelCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>

picard.analysis.directed.InsertSizeMetricsCollector

public class InsertSizeMetricsCollector
extends MultiLevelCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>

Collects InserSizeMetrics on the specified accumulationLevels using

Nested Class Summary

Nested Classes

Modifier and Type	Class and 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)

Field Summary

Fields inherited from class picard.metrics.MultiLevelCollector

UNKNOWN

Constructor Summary

Constructors

Constructor and Description
InsertSizeMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, double minimumPct, java.lang.Integer histogramWidth, double deviations, boolean includeDuplicates)

Method Summary

Modifier and Type	Method and 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 record
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

Methods inherited from class picard.metrics.MultiLevelCollector

addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup

Methods inherited from class java.lang.Object

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

Constructor Detail

InsertSizeMetricsCollector

public InsertSizeMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
                                  java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                                  double minimumPct,
                                  java.lang.Integer histogramWidth,
                                  double deviations,
                                  boolean includeDuplicates)

Method Detail

makeArg

protected picard.analysis.directed.InsertSizeCollectorArgs makeArg(htsjdk.samtools.SAMRecord samRecord,
                                                                   htsjdk.samtools.reference.ReferenceSequence refSeq)

Specified by:

makeArg in class MultiLevelCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>

makeChildCollector

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

Specified by:

makeChildCollector in class MultiLevelCollector<InsertSizeMetrics,java.lang.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 collector

library - If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collector

readGroup - 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

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 class MultiLevelCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>