picard.analysis.RrbsMetricsCollector

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

Field Summary

Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
Constructor Summary

Constructors

Constructor

Description

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

Modifier and Type

Method

Description

protected PerUnitMetricCollector<picard.analysis.RrbsMetrics,Comparable<?>,SAMRecordAndReference>

makeChildCollector(String sample, String library, 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 Details
- RrbsMetricsCollector
  
  public RrbsMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int cQualityThreshold, int nextBaseQualityThreshold, int minReadLength, double maxMismatchRate)
Method Details
- makeChildCollector
  
  protected PerUnitMetricCollector<picard.analysis.RrbsMetrics,Comparable<?>,SAMRecordAndReference> makeChildCollector(String sample, String library, String readGroup)
  
  Description copied from class: MultiLevelCollector
  
  Construct a PerUnitMetricCollector with the given arguments.
  
  Specified by:
  
  makeChildCollector in class MultiLevelCollector<picard.analysis.RrbsMetrics,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

Class RrbsMetricsCollector

Field Summary