Package picard.analysis
Class CollectQualityYieldMetrics.QualityYieldMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- Direct Known Subclasses:
CollectQualityYieldMetrics.QualityYieldMetricsFlow
- Enclosing class:
- CollectQualityYieldMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectQualityYieldMetrics.QualityYieldMetrics
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
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Field Summary
FieldsModifier and TypeFieldDescriptionlong
The total number of bases in all PF readslong
The number of bases in PF reads that achieve quality score 20 or higherlong
The sum of quality scores of all bases in PF reads divided by 20long
The number of bases in PF reads that achieve quality score 30 or higherlong
The number of reads that are PF - pass filterlong
The number of bases in all reads that achieve quality score 20 or higherlong
The sum of quality scores of all bases divided by 20long
The number of bases in all reads that achieve quality score 30 or higherint
The average read length of all the readslong
The total number of bases in all readslong
The total number of reads in the input fileprotected final boolean
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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
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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 -
READ_LENGTH
public int READ_LENGTHThe average read length of all the reads -
TOTAL_BASES
public long TOTAL_BASESThe total number of bases in all reads -
PF_BASES
public long PF_BASESThe total number of bases in all PF reads -
Q20_BASES
public long Q20_BASESThe number of bases in all reads that achieve quality score 20 or higher -
PF_Q20_BASES
public long PF_Q20_BASESThe number of bases in PF reads that achieve quality score 20 or higher -
Q30_BASES
public long Q30_BASESThe number of bases in all reads that achieve quality score 30 or higher -
PF_Q30_BASES
public long PF_Q30_BASESThe number of bases in PF reads that achieve quality score 30 or higher -
Q20_EQUIVALENT_YIELD
public long Q20_EQUIVALENT_YIELDThe sum of quality scores of all bases divided by 20 -
PF_Q20_EQUIVALENT_YIELD
public long PF_Q20_EQUIVALENT_YIELDThe sum of quality scores of all bases in PF reads divided by 20 -
useOriginalQualities
protected final boolean useOriginalQualities
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Constructor Details
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QualityYieldMetrics
public QualityYieldMetrics() -
QualityYieldMetrics
public QualityYieldMetrics(boolean useOriginalQualities)
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Method Details
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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 classMergeableMetricBase
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merge
Description copied from class:MergeableMetricBase
Merge another metric into this one- Overrides:
merge
in classMergeableMetricBase
- Parameters:
other
- metric to merge into this one.
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