Package picard.analysis
Class CollectOxoGMetrics.CpcgMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.CollectOxoGMetrics.CpcgMetrics
- Enclosing class:
CollectOxoGMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static final class CollectOxoGMetrics.CpcgMetrics
extends htsjdk.samtools.metrics.MetricBase
Metrics class for outputs.
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Field Summary
FieldsModifier and TypeFieldDescriptionlong
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the causelong
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.long
The number of alt (A/T) basecalls observed at sites where the genome reference == C.double
The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs.double
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.long
The number of ref basecalls observed at sites where the genome reference == C.The sequence context being reported on.long
The number of alt (A/T) basecalls observed at sites where the genome reference == G.double
The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs.double
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.long
The number of ref basecalls observed at sites where the genome reference == G.The name of the library being assayed.double
The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASESdouble
-10 * log10(OXIDATION_ERROR_RATE)long
The number of reference alleles observed as C in read 1 and G in read 2.long
The number of reference alleles observed as G in read 1 and C in read 2.long
The total number of reference alleles observedThe name of the sample being assayed.long
The total number of basecalls observed at all sites.int
The total number of sites that had at least one base covering them. -
Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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SAMPLE_ALIAS
The name of the sample being assayed. -
LIBRARY
The name of the library being assayed. -
CONTEXT
The sequence context being reported on. -
TOTAL_SITES
public int TOTAL_SITESThe total number of sites that had at least one base covering them. -
TOTAL_BASES
public long TOTAL_BASESThe total number of basecalls observed at all sites. -
REF_NONOXO_BASES
public long REF_NONOXO_BASESThe number of reference alleles observed as C in read 1 and G in read 2. -
REF_OXO_BASES
public long REF_OXO_BASESThe number of reference alleles observed as G in read 1 and C in read 2. -
REF_TOTAL_BASES
public long REF_TOTAL_BASESThe total number of reference alleles observed -
ALT_NONOXO_BASES
public long ALT_NONOXO_BASESThe count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause -
ALT_OXO_BASES
public long ALT_OXO_BASESThe count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage. -
OXIDATION_ERROR_RATE
public double OXIDATION_ERROR_RATEThe oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES -
OXIDATION_Q
public double OXIDATION_Q-10 * log10(OXIDATION_ERROR_RATE) -
C_REF_REF_BASES
public long C_REF_REF_BASESThe number of ref basecalls observed at sites where the genome reference == C. -
G_REF_REF_BASES
public long G_REF_REF_BASESThe number of ref basecalls observed at sites where the genome reference == G. -
C_REF_ALT_BASES
public long C_REF_ALT_BASESThe number of alt (A/T) basecalls observed at sites where the genome reference == C. -
G_REF_ALT_BASES
public long G_REF_ALT_BASESThe number of alt (A/T) basecalls observed at sites where the genome reference == G. -
C_REF_OXO_ERROR_RATE
public double C_REF_OXO_ERROR_RATEThe rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base. -
C_REF_OXO_Q
public double C_REF_OXO_QC_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score. -
G_REF_OXO_ERROR_RATE
public double G_REF_OXO_ERROR_RATEThe rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base. -
G_REF_OXO_Q
public double G_REF_OXO_QG_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
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Constructor Details
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CpcgMetrics
public CpcgMetrics()
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