picard.analysis.artifacts

Class SequencingArtifactMetrics.BaitBiasDetailMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics

Enclosing class:

SequencingArtifactMetrics

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

Bait bias 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.
java.lang.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)).
java.lang.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)).
java.lang.String	SAMPLE_ALIAS

Constructor Summary

Constructors

Constructor and Description
BaitBiasDetailMetrics()

Method Summary

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

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.

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.

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.

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.

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.

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)).

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)).

ERROR_RATE

public double ERROR_RATE

The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).

QSCORE

public double QSCORE

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

Constructor Detail

BaitBiasDetailMetrics

public BaitBiasDetailMetrics()

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.BaitBiasDetailMetrics o)