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