picard.analysis

Class RrbsMetricsCollector

java.lang.Object

picard.metrics.MultiLevelCollector<BEAN,HKEY,SAMRecordAndReference>

picard.metrics.SAMRecordAndReferenceMultiLevelCollector<picard.analysis.RrbsMetrics,java.lang.Comparable<?>>

picard.analysis.RrbsMetricsCollector

public class RrbsMetricsCollector
extends SAMRecordAndReferenceMultiLevelCollector<picard.analysis.RrbsMetrics,java.lang.Comparable<?>>

Field Summary

Fields inherited from class picard.metrics.MultiLevelCollector

UNKNOWN

Constructor Summary

Constructors

Constructor and Description
RrbsMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int cQualityThreshold, int nextBaseQualityThreshold, int minReadLength, double maxMismatchRate)

Method Summary

Modifier and Type	Method and Description
protected PerUnitMetricCollector<picard.analysis.RrbsMetrics,java.lang.Comparable<?>,SAMRecordAndReference>	makeChildCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup) Construct a PerUnitMetricCollector with the given arguments.

Methods inherited from class picard.metrics.SAMRecordAndReferenceMultiLevelCollector

makeArg

Methods inherited from class picard.metrics.MultiLevelCollector

acceptRecord, 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

RrbsMetricsCollector

public RrbsMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
                            java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                            int cQualityThreshold,
                            int nextBaseQualityThreshold,
                            int minReadLength,
                            double maxMismatchRate)

Method Detail

makeChildCollector

protected PerUnitMetricCollector<picard.analysis.RrbsMetrics,java.lang.Comparable<?>,SAMRecordAndReference> makeChildCollector(java.lang.String sample,
                                                                                                                               java.lang.String library,
                                                                                                                               java.lang.String readGroup)

Description copied from class: MultiLevelCollector

Construct a PerUnitMetricCollector with the given arguments.

Specified by:

makeChildCollector in class MultiLevelCollector<picard.analysis.RrbsMetrics,java.lang.Comparable<?>,SAMRecordAndReference>

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