Package picard.analysis.artifacts
Class SequencingArtifactMetrics.BaitBiasDetailMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
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- Enclosing class:
- SequencingArtifactMetrics
public static class SequencingArtifactMetrics.BaitBiasDetailMetrics extends htsjdk.samtools.metrics.MetricBase
Bait bias artifacts broken down by context.
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Field Summary
Fields Modifier and Type Field Description char
ALT_BASE
The (upper-case) alternative base that is called as a result of DNA damage.String
CONTEXT
The sequence context to which the analysis is constrained.double
ERROR_RATE
The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).long
FWD_CXT_ALT_BASES
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.long
FWD_CXT_REF_BASES
The number of REF_BASE:REF_BASE alignments at sites with the given reference context.double
FWD_ERROR_RATE
The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).String
LIBRARY
The name of the library being assayed.double
QSCORE
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).char
REF_BASE
The (upper-case) original base on the reference strand.long
REV_CXT_ALT_BASES
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.long
REV_CXT_REF_BASES
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.double
REV_ERROR_RATE
The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).String
SAMPLE_ALIAS
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Constructor Summary
Constructors Constructor Description BaitBiasDetailMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
calculateDerivedStatistics()
Calculate the error rate given the raw counts.int
compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics o)
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Field Detail
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SAMPLE_ALIAS
public String SAMPLE_ALIAS
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LIBRARY
public String LIBRARY
The name of the library being assayed.
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REF_BASE
public char REF_BASE
The (upper-case) original base on the reference strand.
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ALT_BASE
public char ALT_BASE
The (upper-case) alternative base that is called as a result of DNA damage.
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CONTEXT
public String CONTEXT
The sequence context to which the analysis is constrained.
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FWD_CXT_REF_BASES
public long FWD_CXT_REF_BASES
The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
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FWD_CXT_ALT_BASES
public long FWD_CXT_ALT_BASES
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
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REV_CXT_REF_BASES
public long REV_CXT_REF_BASES
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
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REV_CXT_ALT_BASES
public long REV_CXT_ALT_BASES
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
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FWD_ERROR_RATE
public double FWD_ERROR_RATE
The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).
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REV_ERROR_RATE
public double REV_ERROR_RATE
The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
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ERROR_RATE
public double ERROR_RATE
The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).
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QSCORE
public double QSCORE
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
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Method Detail
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calculateDerivedStatistics
public void calculateDerivedStatistics()
Calculate the error rate given the raw counts. Negative rates are set to MIN_ERROR.
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compareTo
public int compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics o)
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