Package picard.analysis.artifacts
Class SequencingArtifactMetrics.PreAdapterDetailMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
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- Enclosing class:
- SequencingArtifactMetrics
@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class SequencingArtifactMetrics.PreAdapterDetailMetrics extends htsjdk.samtools.metrics.MetricBase
Pre-adapter 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.long
CON_ALT_BASES
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.long
CON_REF_BASES
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.String
CONTEXT
The sequence context to which the analysis is constrained.double
ERROR_RATE
The estimated error rate due to this artifact.String
LIBRARY
The name of the library being assayed.long
PRO_ALT_BASES
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.long
PRO_REF_BASES
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.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.String
SAMPLE_ALIAS
The name of the sample being assayed.
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Constructor Summary
Constructors Constructor Description PreAdapterDetailMetrics()
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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.PreAdapterDetailMetrics o)
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Field Detail
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SAMPLE_ALIAS
public String SAMPLE_ALIAS
The name of the sample being assayed.
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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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PRO_REF_BASES
public long PRO_REF_BASES
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
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PRO_ALT_BASES
public long PRO_ALT_BASES
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
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CON_REF_BASES
public long CON_REF_BASES
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
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CON_ALT_BASES
public long CON_ALT_BASES
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
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ERROR_RATE
public double ERROR_RATE
The estimated error rate due to this artifact. Calculated as max(1e-10, (PRO_ALT_BASES - CON_ALT_BASES) / (PRO_ALT_BASES + PRO_REF_BASES + CON_ALT_BASES + CON_REF_BASES)).
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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.PreAdapterDetailMetrics o)
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