SequencingArtifactMetrics.PreAdapterSummaryMetrics (PICARD JDK API Documentation)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics

Enclosing class:

SequencingArtifactMetrics
```
public static class SequencingArtifactMetrics.PreAdapterSummaryMetrics
extends htsjdk.samtools.metrics.MetricBase
```
Summary analysis of a single pre-adapter artifact. These artifacts occur on the original template strand, before the addition of adapters, so they correlate with read number / orientation in a specific way. For example, the well-known "Oxo-G" artifact occurs when a G on the template strand is oxidized, giving it an affinity for binding to A rather than the usual C. Thus PCR will introduce apparent G>T substitutions in read 1 and C>A in read 2. In the resulting alignments, a given G>T or C>A observation could either be: 1. a true mutation 2. an OxoG artifact 3. some other kind of artifact On average, we assume that 1 and 3 will not display this read number / orientation bias, so their contributions will cancel out in the calculation.

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`	`ARTIFACT_NAME` A "nickname" of this artifact, if it is a known error mode.
`java.lang.String`	`LIBRARY` The name of the library being assayed.
`char`	`REF_BASE` The (upper-case) original base on the reference strand.
`java.lang.String`	`SAMPLE_ALIAS` The name of the sample being assayed.
`double`	`TOTAL_QSCORE` The total Phred-scaled Q-score for this artifact.
`java.lang.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.
`java.lang.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.
`java.lang.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 Summary

Constructors
Constructor and Description

PreAdapterSummaryMetrics()

Constructors
Constructor and Description
`PreAdapterSummaryMetrics()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method and Description

void inferArtifactName()
Label the artifacts corresponding to known error modes.
- 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`inferArtifactName()` Label the artifacts corresponding to known error modes.

- 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.
  - TOTAL_QSCORE
```
public double TOTAL_QSCORE
```
    The total Phred-scaled Q-score for this artifact. A lower Q-score means a higher probability that a REF_BASE:ALT_BASE observation randomly picked from the data will be due to this artifact, rather than a true variant.
  - WORST_CXT
```
public java.lang.String WORST_CXT
```
    The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
  - WORST_CXT_QSCORE
```
public double WORST_CXT_QSCORE
```
    The Q-score for the worst context.
  - WORST_PRE_CXT
```
public java.lang.String WORST_PRE_CXT
```
    The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
  - WORST_PRE_CXT_QSCORE
```
public double WORST_PRE_CXT_QSCORE
```
    The Q-score for the worst pre-context.
  - WORST_POST_CXT
```
public java.lang.String WORST_POST_CXT
```
    The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
  - WORST_POST_CXT_QSCORE
```
public double WORST_POST_CXT_QSCORE
```
    The Q-score for the worst post-context.
  - ARTIFACT_NAME
```
public java.lang.String ARTIFACT_NAME
```
    A "nickname" of this artifact, if it is a known error mode.
- Constructor Detail
  - PreAdapterSummaryMetrics
```
public PreAdapterSummaryMetrics()
```
- Method Detail
  - inferArtifactName
```
public void inferArtifactName()
```
    Label the artifacts corresponding to known error modes.

Class SequencingArtifactMetrics.PreAdapterSummaryMetrics

Field Summary

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

SAMPLE_ALIAS

LIBRARY

REF_BASE

ALT_BASE

TOTAL_QSCORE

WORST_CXT

WORST_CXT_QSCORE

WORST_PRE_CXT

WORST_PRE_CXT_QSCORE

WORST_POST_CXT

WORST_POST_CXT_QSCORE

ARTIFACT_NAME

Constructor Detail

PreAdapterSummaryMetrics

Method Detail

inferArtifactName