Package picard.analysis
Class CollectQualityYieldMetrics.QualityYieldMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
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- Enclosing class:
- CollectQualityYieldMetrics
public static class CollectQualityYieldMetrics.QualityYieldMetrics extends htsjdk.samtools.metrics.MetricBase
A set of metrics used to describe the general quality of a BAM file
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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 reads (will be fixed for a lane)long
TOTAL_BASES
The total number of bases in all readslong
TOTAL_READS
The total number of reads in the input file
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Constructor Summary
Constructors Constructor Description QualityYieldMetrics()
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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 (will be fixed for a lane)
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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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