public class GcBiasMetricsCollector extends MultiLevelCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>
Modifier and Type | Class and Description |
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class |
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector |
UNKNOWN
Constructor and Description |
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GcBiasMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
int[] windowsByGc,
java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
int scanWindowSize,
boolean bisulfite) |
Modifier and Type | Method and Description |
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void |
acceptRecord(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence ref)
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass
this value to all collectors that should include this record
|
protected picard.analysis.GcBiasCollectorArgs |
makeArg(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence ref) |
protected PerUnitMetricCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs> |
makeChildCollector(java.lang.String sample,
java.lang.String library,
java.lang.String readGroup)
Construct a PerUnitMetricCollector with the given arguments.
|
addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
public GcBiasMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite)
protected picard.analysis.GcBiasCollectorArgs makeArg(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
makeArg
in class MultiLevelCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>
protected PerUnitMetricCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs> makeChildCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup)
MultiLevelCollector
makeChildCollector
in class MultiLevelCollector<GcBiasMetrics,java.lang.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 collectorpublic void acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
MultiLevelCollector
acceptRecord
in class MultiLevelCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>