Package picard.analysis.artifacts
Class SequencingArtifactMetrics.PreAdapterDetailMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
- 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
FieldsModifier and TypeFieldDescriptionchar
The (upper-case) alternative base that is called as a result of DNA damage.long
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.long
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.The sequence context to which the analysis is constrained.double
The estimated error rate due to this artifact.The name of the library being assayed.long
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.long
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.double
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).char
The (upper-case) original base on the reference strand.The name of the sample being assayed. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Calculate the error rate given the raw counts.int
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. -
REF_BASE
public char REF_BASEThe (upper-case) original base on the reference strand. -
ALT_BASE
public char ALT_BASEThe (upper-case) alternative base that is called as a result of DNA damage. -
CONTEXT
The sequence context to which the analysis is constrained. -
PRO_REF_BASES
public long PRO_REF_BASESThe number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact. -
PRO_ALT_BASES
public long PRO_ALT_BASESThe number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact. -
CON_REF_BASES
public long CON_REF_BASESThe number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact. -
CON_ALT_BASES
public long CON_ALT_BASESThe number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact. -
ERROR_RATE
public double ERROR_RATEThe 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)). -
QSCORE
public double QSCOREThe Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
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Constructor Details
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PreAdapterDetailMetrics
public PreAdapterDetailMetrics()
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Method Details
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calculateDerivedStatistics
public void calculateDerivedStatistics()Calculate the error rate given the raw counts. Negative rates are set to MIN_ERROR. -
compareTo
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