picard.analysis.artifacts

Class SequencingArtifactMetrics.PreAdapterDetailMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics

Enclosing class:

SequencingArtifactMetrics

public static class SequencingArtifactMetrics.PreAdapterDetailMetrics
extends htsjdk.samtools.metrics.MetricBase

Pre-adapter artifacts broken down by context.

Field Summary

Fields

Modifier and Type	Field and 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.
java.lang.String	CONTEXT The sequence context to which the analysis is constrained.
double	ERROR_RATE The estimated error rate due to this artifact.
java.lang.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.
java.lang.String	SAMPLE_ALIAS The name of the sample being assayed.

Constructor Summary

Constructors

Constructor and Description
PreAdapterDetailMetrics()

Method Summary

Modifier and Type	Method and Description
void	calculateDerivedStatistics() Calculate the error rate given the raw counts.
int	compareTo(SequencingArtifactMetrics.PreAdapterDetailMetrics o)

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

SAMPLE_ALIAS

public java.lang.String SAMPLE_ALIAS

The name of the sample being assayed.

LIBRARY

public java.lang.String LIBRARY

The name of the library being assayed.

REF_BASE

public char REF_BASE

The (upper-case) original base on the reference strand.

ALT_BASE

public char ALT_BASE

The (upper-case) alternative base that is called as a result of DNA damage.

CONTEXT

public java.lang.String CONTEXT

The sequence context to which the analysis is constrained.

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.

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.

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.

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.

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)).

QSCORE

public double QSCORE

The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).

Constructor Detail

PreAdapterDetailMetrics

public PreAdapterDetailMetrics()

Method Detail

calculateDerivedStatistics

public void calculateDerivedStatistics()

Calculate the error rate given the raw counts. Negative rates are set to MIN_ERROR.

compareTo

public int compareTo(SequencingArtifactMetrics.PreAdapterDetailMetrics o)