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
-
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 TypeFieldDescriptionint
The average number of flows in PF readsdouble
The percentage of flows in all reads that achieve quality score 20 or higherdouble
The percentage of flows in all reads that achieve quality score 30 or higherlong
The total number of flows in all PF readslong
The sum of quality scores of all flows in PF reads divided by 20long
The number of flows in PF reads that achieve quality score 20 or higherlong
The number of flows in PF reads that achieve quality score 30 or higherlong
The number of reads that are PF - pass filterlong
The total number of reads in the input file -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Placeholder 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, mergeIfCan
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
-
Field Details
-
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
-
-
Constructor Details
-
QualityYieldMetricsFlow
public QualityYieldMetricsFlow()
-
-
Method Details
-
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 classMergeableMetricBase
-
merge
Description copied from class:MergeableMetricBase
Merge another metric into this one- Overrides:
merge
in classMergeableMetricBase
- Parameters:
other
- metric to merge into this one.
-