public static class SequencingArtifactMetrics.BaitBiasSummaryMetrics
extends htsjdk.samtools.metrics.MetricBase
Modifier and Type | Field | Description |
---|---|---|
char |
ALT_BASE |
The (upper-case) alternative base that is called as a result of DNA damage.
|
String |
ARTIFACT_NAME |
A "nickname" of this artifact, if it is a known error mode.
|
String |
LIBRARY |
The name of the library being assayed.
|
char |
REF_BASE |
The (upper-case) original base on the reference strand.
|
String |
SAMPLE_ALIAS |
The name of the sample being assayed.
|
double |
TOTAL_QSCORE |
The total Phred-scaled Q-score for this artifact.
|
String |
WORST_CXT |
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
|
double |
WORST_CXT_QSCORE |
The Q-score for the worst context.
|
String |
WORST_POST_CXT |
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
|
double |
WORST_POST_CXT_QSCORE |
The Q-score for the worst post-context.
|
String |
WORST_PRE_CXT |
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
|
double |
WORST_PRE_CXT_QSCORE |
The Q-score for the worst pre-context.
|
Constructor | Description |
---|---|
BaitBiasSummaryMetrics() |
Modifier and Type | Method | Description |
---|---|---|
void |
inferArtifactName() |
Label the artifacts corresponding to known error modes.
|
public String SAMPLE_ALIAS
public String LIBRARY
public char REF_BASE
public char ALT_BASE
public double TOTAL_QSCORE
public String WORST_CXT
public double WORST_CXT_QSCORE
public String WORST_PRE_CXT
public double WORST_PRE_CXT_QSCORE
public String WORST_POST_CXT
public double WORST_POST_CXT_QSCORE
public String ARTIFACT_NAME