Package picard.analysis
Class CollectQualityYieldMetrics.QualityYieldMetrics
- 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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- 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
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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 long
PF_BASES
The total number of bases in all PF readslong
PF_Q20_BASES
The number of bases in PF reads that achieve quality score 20 or higherlong
PF_Q20_EQUIVALENT_YIELD
The sum of quality scores of all bases in PF reads divided by 20long
PF_Q30_BASES
The number of bases in PF reads that achieve quality score 30 or higherlong
PF_READS
The number of reads that are PF - pass filterlong
Q20_BASES
The number of bases in all reads that achieve quality score 20 or higherlong
Q20_EQUIVALENT_YIELD
The sum of quality scores of all bases divided by 20long
Q30_BASES
The number of bases in all reads that achieve quality score 30 or higherint
READ_LENGTH
The average read length of all the readslong
TOTAL_BASES
The total number of bases in all readslong
TOTAL_READS
The total number of reads in the input fileprotected boolean
useOriginalQualities
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Constructor Summary
Constructors Constructor Description QualityYieldMetrics()
QualityYieldMetrics(boolean useOriginalQualities)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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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TOTAL_READS
public long TOTAL_READS
The total number of reads in the input file
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PF_READS
public long PF_READS
The number of reads that are PF - pass filter
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READ_LENGTH
public int READ_LENGTH
The average read length of all the reads
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TOTAL_BASES
public long TOTAL_BASES
The total number of bases in all reads
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PF_BASES
public long PF_BASES
The total number of bases in all PF reads
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Q20_BASES
public long Q20_BASES
The number of bases in all reads that achieve quality score 20 or higher
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PF_Q20_BASES
public long PF_Q20_BASES
The number of bases in PF reads that achieve quality score 20 or higher
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Q30_BASES
public long Q30_BASES
The number of bases in all reads that achieve quality score 30 or higher
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PF_Q30_BASES
public long PF_Q30_BASES
The number of bases in PF reads that achieve quality score 30 or higher
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Q20_EQUIVALENT_YIELD
public long Q20_EQUIVALENT_YIELD
The sum of quality scores of all bases divided by 20
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PF_Q20_EQUIVALENT_YIELD
public long PF_Q20_EQUIVALENT_YIELD
The sum of quality scores of all bases in PF reads divided by 20
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useOriginalQualities
protected final boolean useOriginalQualities
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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 classMergeableMetricBase
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merge
public MergeableMetricBase merge(MergeableMetricBase other)
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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