org.biojava3.sequencing.io.fastq
Class FastqTools

java.lang.Object
  extended by org.biojava3.sequencing.io.fastq.FastqTools

public final class FastqTools
extends Object

Utility methods for FASTQ formatted sequences.

Since:
3.0.3

Method Summary
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 createErrorProbabilities(Fastq fastq)
          Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
static QualityFeature createQualityScores(Fastq fastq)
          Create and return a new QualityFeature from the quality scores of 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

createDNASequence

public static DNASequence createDNASequence(Fastq fastq)
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

createDNASequenceWithQualityScores

public static DNASequence createDNASequenceWithQualityScores(Fastq fastq)
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

createDNASequenceWithErrorProbabilities

public static DNASequence createDNASequenceWithErrorProbabilities(Fastq fastq)
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

createDNASequenceWithQualityScoresAndErrorProbabilities

public static DNASequence createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq)
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

createQualityScores

public static QualityFeature 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 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<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