Package org.biojava.bio.program.fastq
Class FastqTools
java.lang.Object
org.biojava.bio.program.fastq.FastqTools
Utility methods for FASTQ formatted sequences.
- Since:
- 1.8.2
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Method Summary
Modifier and TypeMethodDescriptionstatic Fastq
convert
(Fastq fastq, FastqVariant variant) Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.static SymbolList
Create and return a new DNASymbolList
from the specified FASTQ formatted sequence.static Sequence
createDNASequence
(Fastq fastq) Create and return a new DNASequence
from the specified FASTQ formatted sequence.static PhredSequence
createPhredSequence
(Fastq fastq) Create and return a newPhredSequence
from the specified FASTQ formatted sequence.static SymbolList
createQualityScores
(Fastq fastq) Create and return a newSymbolList
of quality scores from the specified FASTQ formatted sequence.static Distribution[]
createSymbolDistribution
(Fastq fastq) Create and return a new array of symbolDistribution
s from the specified FASTQ formatted sequence.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.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 Details
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createDNA
Create and return a new DNASymbolList
from the specified FASTQ formatted sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new DNA
SymbolList
from the specified FASTQ formatted sequence - Throws:
IllegalSymbolException
- if an illegal symbol is found
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createQualityScores
Create and return a newSymbolList
of quality scores from the specified FASTQ formatted sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new
SymbolList
of quality scores from the specified FASTQ formatted sequence - Throws:
IllegalSymbolException
- if an illegal symbol is found
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createDNASequence
Create and return a new DNASequence
from the specified FASTQ formatted sequence.- Parameters:
fastq
- FASTQ formatted sequence, must not be null- Returns:
- a new
Sequence
from the specified FASTQ formatted sequence - Throws:
IllegalSymbolException
- if an illegal symbol is found
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createPhredSequence
public static PhredSequence createPhredSequence(Fastq fastq) throws IllegalAlphabetException, IllegalSymbolException Create and return a newPhredSequence
from the specified FASTQ formatted sequence. Only Sanger variant FASTQ formatted sequences are supported.- Parameters:
fastq
- FASTQ formatted sequence, must not be null and must be Sanger variant- Returns:
- a new
PhredSequence
from the specified FASTQ formatted sequence - Throws:
IllegalAlphabetException
- if an illegal alphabet is usedIllegalSymbolException
- if an illegal symbol is found
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createSymbolDistribution
public static Distribution[] createSymbolDistribution(Fastq fastq) throws IllegalAlphabetException, IllegalSymbolException Create and return a new array of symbolDistribution
s from the specified FASTQ formatted sequence. Only Sanger variant FASTQ formatted sequences are supported.- Parameters:
fastq
- FASTQ formatted sequence, must not be null and must be Sanger variant- Returns:
- a new array of symbol
Distribution
s from the specified FASTQ formatted sequence - Throws:
IllegalAlphabetException
- if an illegal alphabet is usedIllegalSymbolException
- if an illegal symbol is found
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qualityScores
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
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
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
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
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:
- 1.9.3
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