Package picard.analysis
Class CollectQualityYieldMetricsSNVQ.QualityYieldMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetricsSNVQ.QualityYieldMetrics
- Enclosing class:
CollectQualityYieldMetricsSNVQ
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectQualityYieldMetricsSNVQ.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 TypeFieldDescriptionprotected final String
double
The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filterdouble
The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filterdouble
The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filterdouble
The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filterdouble
The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filterdouble
The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filterdouble
The percentage of SNVQ values in all reads that achieve quality score 20 or higherdouble
The percentage of SNVQ values in all reads that achieve quality score 20 or higherdouble
The percentage of SNVQ values in all reads that achieve quality score 30 or higherdouble
The percentage of SNVQ values in all reads that achieve quality score 30 or higherdouble
The percentage of SNVQ values in all reads that achieve quality score 40 or higherdouble
The percentage of SNVQ values in all reads that achieve quality score 40 or higherlong
The total number of bases in all PF readslong
The number of bases in PF reads that achieve quality score 20 or higherlong
The number of SNVQ values in PF reads that achieve quality score 20 or higherlong
The number of bases in PF reads that achieve quality score 30 or higherlong
The number of SNVQ values in PF reads that achieve quality score 30 or higherlong
The number of bases in PF reads that achieve quality score 40 or higherlong
The number of SNVQ values in PF reads that achieve quality score 40 or higherlong
The number of reads that are PF - pass filterlong
The total number of SNVQ values in all PF readslong
The number of bases in all reads that achieve quality score 20 or higherlong
The number of SNVQ values in all reads that achieve quality score 20 or higherlong
The number of bases in all reads that achieve quality score 30 or higherlong
The number of SNVQ values in all reads that achieve quality score 30 or higherlong
The number of bases in all reads that achieve quality score 40 or higherlong
The number of SNVQ values in all reads that achieve quality score 40 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 filelong
The total number of SNVQ values in all reads -
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 -
Q40_BASES
public long Q40_BASESThe number of bases in all reads that achieve quality score 40 or higher -
PF_Q40_BASES
public long PF_Q40_BASESThe number of bases in PF reads that achieve quality score 40 or higher -
PCT_Q20_BASES
public double PCT_Q20_BASESThe percentage of SNVQ values in all reads that achieve quality score 20 or higher -
PCT_Q30_BASES
public double PCT_Q30_BASESThe percentage of SNVQ values in all reads that achieve quality score 30 or higher -
PCT_Q40_BASES
public double PCT_Q40_BASESThe percentage of SNVQ values in all reads that achieve quality score 40 or higher -
PCT_PF_Q20_BASES
public double PCT_PF_Q20_BASESThe percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter -
PCT_PF_Q30_BASES
public double PCT_PF_Q30_BASESThe percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter -
PCT_PF_Q40_BASES
public double PCT_PF_Q40_BASESThe percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter -
TOTAL_SNVQ
public long TOTAL_SNVQThe total number of SNVQ values in all reads -
PF_SNVQ
public long PF_SNVQThe total number of SNVQ values in all PF reads -
Q20_SNVQ
public long Q20_SNVQThe number of SNVQ values in all reads that achieve quality score 20 or higher -
PF_Q20_SNVQ
public long PF_Q20_SNVQThe number of SNVQ values in PF reads that achieve quality score 20 or higher -
Q30_SNVQ
public long Q30_SNVQThe number of SNVQ values in all reads that achieve quality score 30 or higher -
PF_Q30_SNVQ
public long PF_Q30_SNVQThe number of SNVQ values in PF reads that achieve quality score 30 or higher -
Q40_SNVQ
public long Q40_SNVQThe number of SNVQ values in all reads that achieve quality score 40 or higher -
PF_Q40_SNVQ
public long PF_Q40_SNVQThe number of SNVQ values in PF reads that achieve quality score 40 or higher -
PCT_Q20_SNVQ
public double PCT_Q20_SNVQThe percentage of SNVQ values in all reads that achieve quality score 20 or higher -
PCT_Q30_SNVQ
public double PCT_Q30_SNVQThe percentage of SNVQ values in all reads that achieve quality score 30 or higher -
PCT_Q40_SNVQ
public double PCT_Q40_SNVQThe percentage of SNVQ values in all reads that achieve quality score 40 or higher -
PCT_PF_Q20_SNVQ
public double PCT_PF_Q20_SNVQThe percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter -
PCT_PF_Q30_SNVQ
public double PCT_PF_Q30_SNVQThe percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter -
PCT_PF_Q40_SNVQ
public double PCT_PF_Q40_SNVQThe percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter -
alternateQualityAttribute
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Constructor Details
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QualityYieldMetrics
public QualityYieldMetrics() -
QualityYieldMetrics
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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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