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 Modifier and Type Class Description class
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
-
Field Summary
-
Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
-
-
Constructor Summary
Constructors Constructor Description GcBiasMetricsCollector(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
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected 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 Detail
-
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 Detail
-
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,picard.analysis.GcBiasCollectorArgs> makeChildCollector(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
-
-