<T extends Appendable> T |
FastqWriter.append(T appendable,
Fastq... fastq) |
Append the specified FASTQ formatted sequences to the specified appendable.
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static Fastq |
FastqTools.convert(Fastq fastq,
FastqVariant variant) |
Convert the specified FASTQ formatted sequence to the
specified FASTQ sequence format variant.
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protected Fastq |
IlluminaFastqWriter.convert(Fastq fastq) |
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protected Fastq |
SangerFastqWriter.convert(Fastq fastq) |
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protected Fastq |
SolexaFastqWriter.convert(Fastq fastq) |
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static DNASequence |
FastqTools.createDNASequence(Fastq fastq) |
Create and return a new DNASequence from the specified FASTQ formatted sequence.
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static DNASequence |
FastqTools.createDNASequenceWithErrorProbabilities(Fastq fastq) |
Create and return a new DNASequence with error probabilities from the specified
FASTQ formatted sequence.
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static DNASequence |
FastqTools.createDNASequenceWithQualityScores(Fastq fastq) |
Create and return a new DNASequence with quality scores from the specified
FASTQ formatted sequence.
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static DNASequence |
FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq) |
Create and return a new DNASequence with quality scores and error probabilities from the
specified FASTQ formatted sequence.
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static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound> |
FastqTools.createErrorProbabilities(Fastq fastq) |
Create and return a new QuantityFeature from the error probabilities of the specified
FASTQ formatted sequence.
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static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound> |
FastqTools.createQualityScores(Fastq fastq) |
Create and return a new QualityFeature from the quality scores of the specified
FASTQ formatted sequence.
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static Iterable<Number> |
FastqTools.errorProbabilities(Fastq fastq) |
Return the error probabilities from the specified FASTQ formatted sequence.
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static double[] |
FastqTools.errorProbabilities(Fastq fastq,
double[] errorProbabilities) |
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
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void |
StreamListener.fastq(Fastq fastq) |
Notify this listener of a FASTQ formatted sequence.
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static Iterable<Number> |
FastqTools.qualityScores(Fastq fastq) |
Return the quality scores from the specified FASTQ formatted sequence.
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static int[] |
FastqTools.qualityScores(Fastq fastq,
int[] qualityScores) |
Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.
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void |
FastqWriter.write(File file,
Fastq... fastq) |
Write the specified FASTQ formatted sequences to the specified file.
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void |
FastqWriter.write(OutputStream outputStream,
Fastq... fastq) |
Write the specified FASTQ formatted sequences to the specified output stream.
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