Package picard.analysis
Class CollectQualityYieldMetricsSNVQ.QualityYieldMetricsCollector
java.lang.Object
picard.analysis.CollectQualityYieldMetricsSNVQ.QualityYieldMetricsCollector
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CollectQualityYieldMetricsSNVQ
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionQualityYieldMetricsCollector
(String alternateQualityAttribute, boolean includeSecondaryAlignments, boolean includeSupplementalAlignments) -
Method Summary
Modifier and TypeMethodDescriptionvoid
acceptRecord
(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) void
addHistograms
(htsjdk.samtools.metrics.MetricsFile<CollectQualityYieldMetricsSNVQ.QualityYieldMetrics, Integer> metricsFile) void
addMetricsToFile
(htsjdk.samtools.metrics.MetricsFile<CollectQualityYieldMetricsSNVQ.QualityYieldMetrics, Integer> metricsFile) void
finish()
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Field Details
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includeSupplementalAlignments
public final boolean includeSupplementalAlignments
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Constructor Details
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QualityYieldMetricsCollector
public QualityYieldMetricsCollector(String alternateQualityAttribute, boolean includeSecondaryAlignments, boolean includeSupplementalAlignments)
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Method Details
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acceptRecord
public void acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) -
finish
public void finish() -
addMetricsToFile
public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<CollectQualityYieldMetricsSNVQ.QualityYieldMetrics, Integer> metricsFile) -
addHistograms
public void addHistograms(htsjdk.samtools.metrics.MetricsFile<CollectQualityYieldMetricsSNVQ.QualityYieldMetrics, Integer> metricsFile)
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