Package picard.analysis
Class CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
- Enclosing class:
CollectQualityYieldMetricsFlow
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
extends MergeableMetricBase
A set of metrics used to describe the general quality of a BAM file
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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 TypeFieldDescriptionintThe average number of flows in PF readsdoubleThe percentage of flows in all reads that achieve quality score 20 or higherdoubleThe percentage of flows in all reads that achieve quality score 30 or higherlongThe total number of flows in all PF readslongThe sum of quality scores of all flows in PF reads divided by 20longThe number of flows in PF reads that achieve quality score 20 or higherlongThe number of flows in PF reads that achieve quality score 30 or higherlongThe number of reads that are PF - pass filterlongThe total number of reads in the input file -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidPlaceholder 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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TOTAL_READS
public long TOTAL_READSThe total number of reads in the input file -
PF_READS
public long PF_READSThe number of reads that are PF - pass filter -
MEAN_PF_READ_NUMBER_OF_FLOWS
public int MEAN_PF_READ_NUMBER_OF_FLOWSThe average number of flows in PF reads -
PF_FLOWS
public long PF_FLOWSThe total number of flows in all PF reads -
PF_Q20_FLOWS
public long PF_Q20_FLOWSThe number of flows in PF reads that achieve quality score 20 or higher -
PCT_PF_Q20_FLOWS
public double PCT_PF_Q20_FLOWSThe percentage of flows in all reads that achieve quality score 20 or higher -
PF_Q30_FLOWS
public long PF_Q30_FLOWSThe number of flows in PF reads that achieve quality score 30 or higher -
PCT_PF_Q30_FLOWS
public double PCT_PF_Q30_FLOWSThe percentage of flows in all reads that achieve quality score 30 or higher -
PF_Q20_EQUIVALENT_YIELD
public long PF_Q20_EQUIVALENT_YIELDThe sum of quality scores of all flows in PF reads divided by 20
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Constructor Details
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QualityYieldMetricsFlow
public QualityYieldMetricsFlow()
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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 classMergeableMetricBase
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merge
Description copied from class:MergeableMetricBaseMerge another metric into this one- Overrides:
mergein classMergeableMetricBase- Parameters:
other- metric to merge into this one.
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