Package picard.analysis
Class GcBiasMetricsCollector
java.lang.Object
picard.metrics.MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
picard.analysis.GcBiasMetricsCollector
public class GcBiasMetricsCollector
extends MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
Calculates GC Bias Metrics on multiple levels
Created by kbergin on 3/23/15.
-
Nested Class Summary
Nested Classes -
Field Summary
Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
-
Constructor Summary
ConstructorsConstructorDescriptionGcBiasMetricsCollector
(Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite) GcBiasMetricsCollector
(Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite, boolean ignoreDuplicates) -
Method Summary
Modifier and TypeMethodDescriptionprotected picard.analysis.GcBiasCollectorArgs
makeArg
(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) protected PerUnitMetricCollector<GcBiasMetrics,
Integer, picard.analysis.GcBiasCollectorArgs> makeChildCollector
(String sample, String library, String readGroup) Construct a PerUnitMetricCollector with the given arguments.Methods inherited from class picard.metrics.MultiLevelCollector
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
-
Constructor Details
-
GcBiasMetricsCollector
public GcBiasMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite) -
GcBiasMetricsCollector
public GcBiasMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite, boolean ignoreDuplicates)
-
-
Method Details
-
makeArg
protected picard.analysis.GcBiasCollectorArgs makeArg(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) - Specified by:
makeArg
in classMultiLevelCollector<GcBiasMetrics,
Integer, picard.analysis.GcBiasCollectorArgs>
-
makeChildCollector
protected PerUnitMetricCollector<GcBiasMetrics,Integer, makeChildCollectorpicard.analysis.GcBiasCollectorArgs> (String sample, String library, String readGroup) Description copied from class:MultiLevelCollector
Construct a PerUnitMetricCollector with the given arguments.- Specified by:
makeChildCollector
in classMultiLevelCollector<GcBiasMetrics,
Integer, picard.analysis.GcBiasCollectorArgs> - 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
-