Class FastqTools


  • public final class FastqTools
    extends Object
    Utility methods for FASTQ formatted sequences.
    Since:
    3.0.3
    • Method Detail

      • qualityScores

        public static Iterable<NumberqualityScores​(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<NumbererrorProbabilities​(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