public class GcBiasMetricsCollector extends MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
| Modifier and Type | Class and Description |
|---|---|
class |
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector |
UNKNOWN| Constructor and 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) |
| Modifier and Type | Method and 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.
|
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setuppublic GcBiasMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite)
public GcBiasMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite, boolean ignoreDuplicates)
protected picard.analysis.GcBiasCollectorArgs makeArg(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence ref)
makeArg in class MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>protected PerUnitMetricCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs> makeChildCollector(String sample, String library, String readGroup)
MultiLevelCollectormakeChildCollector in class MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>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