Package org.biojava.nbio.genome.io.fastq
Class FastqTools
- java.lang.Object
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- org.biojava.nbio.genome.io.fastq.FastqTools
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public final class FastqTools extends Object
Utility methods for FASTQ formatted sequences.- Since:
- 3.0.3
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static Fastq
convert(Fastq fastq, FastqVariant variant)
Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.static DNASequence
createDNASequence(Fastq fastq)
Create and return a newDNASequence
from the specified FASTQ formatted sequence.static DNASequence
createDNASequenceWithErrorProbabilities(Fastq fastq)
Create and return a newDNASequence
with error probabilities from the specified FASTQ formatted sequence.static DNASequence
createDNASequenceWithQualityScores(Fastq fastq)
Create and return a newDNASequence
with quality scores from the specified FASTQ formatted sequence.static DNASequence
createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq)
Create and return a newDNASequence
with quality scores and error probabilities from the specified FASTQ formatted sequence.static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>
createErrorProbabilities(Fastq fastq)
Create and return a newQuantityFeature
from the error probabilities of the specified FASTQ formatted sequence.static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>
createQualityScores(Fastq fastq)
Create and return a newQualityFeature
from the quality scores of the specified FASTQ formatted sequence.static Iterable<Number>
errorProbabilities(Fastq fastq)
Return the error probabilities from the specified FASTQ formatted sequence.static double[]
errorProbabilities(Fastq fastq, double[] errorProbabilities)
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.static Iterable<Number>
qualityScores(Fastq fastq)
Return the quality scores from the specified FASTQ formatted sequence.static int[]
qualityScores(Fastq fastq, int[] qualityScores)
Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.
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Method Detail
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createDNASequence
public static DNASequence createDNASequence(Fastq fastq) throws CompoundNotFoundException
Create and return a newDNASequence
from the specified FASTQ formatted sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new
DNASequence
from the specified FASTQ formatted sequence - Throws:
CompoundNotFoundException
- if DNA sequence in fastq contains unrecognised compounds
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createDNASequenceWithQualityScores
public static DNASequence createDNASequenceWithQualityScores(Fastq fastq) throws CompoundNotFoundException
Create and return a newDNASequence
with quality scores from the specified FASTQ formatted sequence. The quality scores are stored in aQualityFeature
with a type"qualityScores"
the same length as the sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new
DNASequence
with quality scores from the specified FASTQ formatted sequence - Throws:
CompoundNotFoundException
- if DNA sequence in fastq contains unrecognised compounds
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createDNASequenceWithErrorProbabilities
public static DNASequence createDNASequenceWithErrorProbabilities(Fastq fastq) throws CompoundNotFoundException
Create and return a newDNASequence
with error probabilities from the specified FASTQ formatted sequence. The error probabilities are stored in aQuantityFeature
with a type"errorProbabilities"
the same length as the sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new
DNASequence
with error probabilities from the specified FASTQ formatted sequence - Throws:
CompoundNotFoundException
- if DNA sequence in fastq contains unrecognised compounds
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createDNASequenceWithQualityScoresAndErrorProbabilities
public static DNASequence createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq) throws CompoundNotFoundException
Create and return a newDNASequence
with quality scores and error probabilities from the specified FASTQ formatted sequence. The quality scores are stored in aQualityFeature
with a type"qualityScores"
the same length as the sequence and the error probabilities are stored in aQuantityFeature
with a type"errorProbabilities"
the same length as the sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new
DNASequence
with quality scores and error probabilities from the specified FASTQ formatted sequence - Throws:
CompoundNotFoundException
- if DNA sequence in fastq contains unrecognised compounds
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createQualityScores
public static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound> createQualityScores(Fastq fastq)
Create and return a newQualityFeature
from the quality scores of the specified FASTQ formatted sequence. The quality scores feature has a type"qualityScores"
and will be the same length as the sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new
QualityFeature
from the quality scores of the specified FASTQ formatted sequence
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createErrorProbabilities
public static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound> createErrorProbabilities(Fastq fastq)
Create and return a newQuantityFeature
from the error probabilities of the specified FASTQ formatted sequence. The error probabilities feature has a type"errorProbabilities"
and will be the same length as the sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new
QualityFeature
from the error probabilities of the specified FASTQ formatted sequence
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qualityScores
public static Iterable<Number> qualityScores(Fastq fastq)
Return the quality scores from the specified FASTQ formatted sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- the quality scores from the specified FASTQ formatted sequence
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qualityScores
public static int[] qualityScores(Fastq fastq, int[] qualityScores)
Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.- Parameters:
fastq
- FASTQ formatted sequence, must not be nullqualityScores
- int array of quality scores, must not be null and must be the same length as the FASTQ formatted sequence quality- Returns:
- the specified int array of quality scores
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errorProbabilities
public static Iterable<Number> errorProbabilities(Fastq fastq)
Return the error probabilities from the specified FASTQ formatted sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- the error probabilities from the specified FASTQ formatted sequence
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errorProbabilities
public static double[] errorProbabilities(Fastq fastq, double[] errorProbabilities)
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.- Parameters:
fastq
- FASTQ formatted sequence, must not be nullerrorProbabilities
- double array of error probabilities, must not be null and must be the same length as the FASTQ formatted sequence quality- Returns:
- the specified double array of error probabilities
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convert
public static Fastq convert(Fastq fastq, FastqVariant variant)
Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.- Parameters:
fastq
- FASTQ formatted sequence, must not be nullvariant
- FASTQ sequence format variant, must not be null- Returns:
- the specified FASTQ formatted sequence converted to the specified FASTQ sequence format variant
- Since:
- 4.2
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