Package picard.analysis
Class CollectQualityYieldMetrics.QualityYieldMetricsFlow
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
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- picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
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- Enclosing class:
- CollectQualityYieldMetrics
public static class CollectQualityYieldMetrics.QualityYieldMetricsFlow extends CollectQualityYieldMetrics.QualityYieldMetrics
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
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Field Summary
Fields Modifier and Type Field Description protected picard.analysis.HistogramGenerator
histogramGenerator
long
READ_LENGTH_AVG_Q_ABOVE_25
The length of the longest interval on the reads where the average quality per-base is above (Q25)long
READ_LENGTH_AVG_Q_ABOVE_30
The 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
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Constructor Summary
Constructors Constructor Description QualityYieldMetricsFlow()
QualityYieldMetricsFlow(boolean useOriginalBaseQualities)
QualityYieldMetricsFlow(boolean useOriginalBaseQualities, picard.analysis.HistogramGenerator hg)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
addRecordToHistogramGenerator(htsjdk.samtools.SAMRecord rec)
void
calculateDerivedFields()
Placeholder method that will calculate the derived fields from the other ones.MergeableMetricBase
merge(MergeableMetricBase other)
Merge another metric into this one-
Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, mergeIfCan
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Field Detail
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READ_LENGTH_AVG_Q_ABOVE_30
public long READ_LENGTH_AVG_Q_ABOVE_30
The length of the longest interval on the reads where the average quality per-base is above (Q30)
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READ_LENGTH_AVG_Q_ABOVE_25
public long READ_LENGTH_AVG_Q_ABOVE_25
The length of the longest interval on the reads where the average quality per-base is above (Q25)
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histogramGenerator
protected final picard.analysis.HistogramGenerator histogramGenerator
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Method Detail
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calculateDerivedFields
public void calculateDerivedFields()
Description copied from class:MergeableMetricBase
Placeholder 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:
calculateDerivedFields
in classCollectQualityYieldMetrics.QualityYieldMetrics
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merge
public MergeableMetricBase merge(MergeableMetricBase other)
Description copied from class:MergeableMetricBase
Merge another metric into this one- Overrides:
merge
in 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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