Package | Description |
---|---|
org.biojava.bio.program.fastq |
FASTQ and variants sequence format IO.
|
Modifier and Type | Method and Description |
---|---|
FastqBuilder |
FastqBuilder.appendQuality(String quality)
Return this FASTQ formatted sequence builder configured with the specified quality scores
appended to its current quality scores.
|
FastqBuilder |
FastqBuilder.appendSequence(String sequence)
Return this FASTQ formatted sequence builder configured with the specified sequence
appended to its current sequence.
|
FastqBuilder |
FastqBuilder.withDescription(String description)
Return this FASTQ formatted sequence builder configured with the specified description.
|
FastqBuilder |
FastqBuilder.withQuality(String quality)
Return this FASTQ formatted sequence builder configured with the specified quality scores.
|
FastqBuilder |
FastqBuilder.withSequence(String sequence)
Return this FASTQ formatted sequence builder configured with the specified sequence.
|
FastqBuilder |
FastqBuilder.withVariant(FastqVariant variant)
Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.
|
Modifier and Type | Method and Description |
---|---|
protected void |
SangerFastqReader.validateDescription(FastqBuilder builder,
String description,
int lineNumber)
Validate the specified description.
|
protected void |
SolexaFastqReader.validateDescription(FastqBuilder builder,
String description,
int lineNumber)
Validate the specified description.
|
protected void |
IlluminaFastqReader.validateDescription(FastqBuilder builder,
String description,
int lineNumber)
Validate the specified description.
|
protected void |
SangerFastqReader.validateQuality(FastqBuilder builder,
String quality,
int lineNumber)
Validate the specified quality scores.
|
protected void |
SolexaFastqReader.validateQuality(FastqBuilder builder,
String quality,
int lineNumber)
Validate the specified quality scores.
|
protected void |
IlluminaFastqReader.validateQuality(FastqBuilder builder,
String quality,
int lineNumber)
Validate the specified quality scores.
|
protected void |
SangerFastqReader.validateRepeatDescription(FastqBuilder builder,
String repeatDescription,
int lineNumber)
Validate the specified repeat description.
|
protected void |
SolexaFastqReader.validateRepeatDescription(FastqBuilder builder,
String repeatDescription,
int lineNumber)
Validate the specified repeat description.
|
protected void |
IlluminaFastqReader.validateRepeatDescription(FastqBuilder builder,
String repeatDescription,
int lineNumber)
Validate the specified repeat description.
|
protected void |
SangerFastqReader.validateSequence(FastqBuilder builder,
String sequence,
int lineNumber)
Validate the specified sequence.
|
protected void |
SolexaFastqReader.validateSequence(FastqBuilder builder,
String sequence,
int lineNumber)
Validate the specified sequence.
|
protected void |
IlluminaFastqReader.validateSequence(FastqBuilder builder,
String sequence,
int lineNumber)
Validate the specified sequence.
|