Package org.biojava.bio.program.fastq

Class FastqTools

java.lang.Object

org.biojava.bio.program.fastq.FastqTools

public final class FastqTools
extends Object

Utility methods for FASTQ formatted sequences.

Since:

1.8.2

Method Summary

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 SymbolList	createDNA(Fastq fastq)	Create and return a new DNA SymbolList from the specified FASTQ formatted sequence.
static Sequence	createDNASequence(Fastq fastq)	Create and return a new DNA Sequence from the specified FASTQ formatted sequence.
static PhredSequence	createPhredSequence(Fastq fastq)	Create and return a new PhredSequence from the specified FASTQ formatted sequence.
static SymbolList	createQualityScores(Fastq fastq)	Create and return a new SymbolList of quality scores from the specified FASTQ formatted sequence.
static Distribution[]	createSymbolDistribution(Fastq fastq)	Create and return a new array of symbol Distributions from the specified FASTQ formatted sequence.
static Iterable<Double>	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<Integer>	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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

createDNA

public static SymbolList createDNA(Fastq fastq)
                            throws IllegalSymbolException

Create and return a new DNA SymbolList 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

createQualityScores

public static SymbolList createQualityScores(Fastq fastq)
                                      throws IllegalSymbolException

Create and return a new SymbolList 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

createDNASequence

public static Sequence createDNASequence(Fastq fastq)
                                  throws IllegalSymbolException

Create and return a new DNA Sequence 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

createPhredSequence

public static PhredSequence createPhredSequence(Fastq fastq)
                                         throws IllegalAlphabetException,
                                                IllegalSymbolException

Create and return a new PhredSequence 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 used

IllegalSymbolException - if an illegal symbol is found

createSymbolDistribution

public static Distribution[] createSymbolDistribution(Fastq fastq)
                                               throws IllegalAlphabetException,
                                                      IllegalSymbolException

Create and return a new array of symbol Distributions 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 Distributions from the specified FASTQ formatted sequence

Throws:

IllegalAlphabetException - if an illegal alphabet is used

IllegalSymbolException - if an illegal symbol is found

qualityScores

public static Iterable<Integer> 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

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 null

qualityScores - 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

errorProbabilities

public static Iterable<Double> 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

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 null

errorProbabilities - 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

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 null

variant - 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