Package picard.analysis
Class RrbsMetricsCollector
java.lang.Object
picard.metrics.MultiLevelCollector<picard.analysis.RrbsMetrics,Comparable<?>,SAMRecordAndReference>
picard.metrics.SAMRecordAndReferenceMultiLevelCollector<picard.analysis.RrbsMetrics,Comparable<?>>
picard.analysis.RrbsMetricsCollector
public class RrbsMetricsCollector
extends SAMRecordAndReferenceMultiLevelCollector<picard.analysis.RrbsMetrics,Comparable<?>>
-
Field Summary
Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
-
Constructor Summary
ConstructorsConstructorDescriptionRrbsMetricsCollector
(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int cQualityThreshold, int nextBaseQualityThreshold, int minReadLength, double maxMismatchRate) -
Method Summary
Modifier and TypeMethodDescriptionprotected 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
-
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<?>, makeChildCollectorSAMRecordAndReference> (String sample, String library, String readGroup) Description copied from class:MultiLevelCollector
Construct a PerUnitMetricCollector with the given arguments.- Specified by:
makeChildCollector
in classMultiLevelCollector<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 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
-