Package org.biojava.nbio.genome.io.fastq

Class FastqTools

java.lang.Object

org.biojava.nbio.genome.io.fastq.FastqTools

public final class FastqTools
extends Object

Utility methods for FASTQ formatted sequences.

Since:

3.0.3

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 DNASequence	createDNASequence(Fastq fastq)	Create and return a new DNASequence from the specified FASTQ formatted sequence.
static DNASequence	createDNASequenceWithErrorProbabilities(Fastq fastq)	Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.
static DNASequence	createDNASequenceWithQualityScores(Fastq fastq)	Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.
static DNASequence	createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq)	Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.
static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	createErrorProbabilities(Fastq fastq)	Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	createQualityScores(Fastq fastq)	Create and return a new QualityFeature 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.

Methods inherited from class java.lang.Object

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

Method Detail

createDNASequence

public static DNASequence createDNASequence(Fastq fastq)
                                     throws CompoundNotFoundException

Create and return a new DNASequence 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

createDNASequenceWithQualityScores

public static DNASequence createDNASequenceWithQualityScores(Fastq fastq)
                                                      throws CompoundNotFoundException

Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence. The quality scores are stored in a QualityFeature 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

createDNASequenceWithErrorProbabilities

public static DNASequence createDNASequenceWithErrorProbabilities(Fastq fastq)
                                                           throws CompoundNotFoundException

Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence. The error probabilities are stored in a QuantityFeature 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

createDNASequenceWithQualityScoresAndErrorProbabilities

public static DNASequence createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq)
                                                                           throws CompoundNotFoundException

Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence. The quality scores are stored in a QualityFeature with a type "qualityScores" the same length as the sequence and the error probabilities are stored in a QuantityFeature 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

createQualityScores

public static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound> createQualityScores(Fastq fastq)

Create and return a new QualityFeature 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

createErrorProbabilities

public static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound> createErrorProbabilities(Fastq fastq)

Create and return a new QuantityFeature 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

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

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<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

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:

4.2