Package picard.analysis
Class CollectQualityYieldMetrics.QualityYieldMetricsFlow
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- Enclosing class:
- CollectQualityYieldMetrics
public static class CollectQualityYieldMetrics.QualityYieldMetricsFlow
extends CollectQualityYieldMetrics.QualityYieldMetrics
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Nested Class Summary
Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue -
Field Summary
FieldsModifier and TypeFieldDescriptionprotected final picard.analysis.HistogramGeneratorlongThe length of the longest interval on the reads where the average quality per-base is above (Q25)longThe length of the longest interval on the reads where the average quality per-base is above (Q30)Fields inherited from class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
PF_BASES, PF_Q20_BASES, PF_Q20_EQUIVALENT_YIELD, PF_Q30_BASES, PF_READS, Q20_BASES, Q20_EQUIVALENT_YIELD, Q30_BASES, READ_LENGTH, TOTAL_BASES, TOTAL_READS, useOriginalQualities -
Constructor Summary
ConstructorsConstructorDescriptionQualityYieldMetricsFlow(boolean useOriginalBaseQualities) QualityYieldMetricsFlow(boolean useOriginalBaseQualities, picard.analysis.HistogramGenerator hg) -
Method Summary
Modifier and TypeMethodDescriptionprotected voidaddRecordToHistogramGenerator(htsjdk.samtools.SAMRecord rec) voidPlaceholder method that will calculate the derived fields from the other ones.merge(MergeableMetricBase other) Merge another metric into this oneMethods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, mergeIfCanMethods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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READ_LENGTH_AVG_Q_ABOVE_30
public long READ_LENGTH_AVG_Q_ABOVE_30The length of the longest interval on the reads where the average quality per-base is above (Q30) -
READ_LENGTH_AVG_Q_ABOVE_25
public long READ_LENGTH_AVG_Q_ABOVE_25The length of the longest interval on the reads where the average quality per-base is above (Q25) -
histogramGenerator
protected final picard.analysis.HistogramGenerator histogramGenerator
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Constructor Details
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QualityYieldMetricsFlow
public QualityYieldMetricsFlow() -
QualityYieldMetricsFlow
public QualityYieldMetricsFlow(boolean useOriginalBaseQualities) -
QualityYieldMetricsFlow
public QualityYieldMetricsFlow(boolean useOriginalBaseQualities, picard.analysis.HistogramGenerator hg)
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Method Details
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calculateDerivedFields
public void calculateDerivedFields()Description copied from class:MergeableMetricBasePlaceholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated withNoMergingKeepsValue.- Overrides:
calculateDerivedFieldsin classCollectQualityYieldMetrics.QualityYieldMetrics
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merge
Description copied from class:MergeableMetricBaseMerge another metric into this one- Overrides:
mergein classCollectQualityYieldMetrics.QualityYieldMetrics- Parameters:
other- metric to merge into this one.
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addRecordToHistogramGenerator
protected void addRecordToHistogramGenerator(htsjdk.samtools.SAMRecord rec)
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