Class SolexaQualityConverter


  • public class SolexaQualityConverter
    extends Object
    Optimized method for converting Solexa ASCII qualities into Phred scores. Pre-computes all values in order to eliminate repeated computation.
    • Field Detail

      • SOLEXA_ADDEND

        public static final int SOLEXA_ADDEND
        This value is added to a Solexa quality score to make it printable ASCII
        See Also:
        Constant Field Values
      • PHRED_ADDEND

        public static final int PHRED_ADDEND
        This value is added to a Phred scord to make it printable ASCII
        See Also:
        Constant Field Values
      • ILLUMINA_TO_PHRED_SUBTRAHEND

        public static final int ILLUMINA_TO_PHRED_SUBTRAHEND
        This value is removed from an Illumina 1.8 quality score to make it a Phred score
        See Also:
        Constant Field Values
    • Method Detail

      • solexaCharToPhredBinary

        public byte solexaCharToPhredBinary​(byte solexaQuality)
        Convert a solexa quality ASCII character into a phred score.
      • getSolexaToPhredConversionTable

        public byte[] getSolexaToPhredConversionTable()
        Returns:
        a byte array that can be indexed by Solexa ASCII quality, with value of corresponding Phred score. Elements 0-63 are invalid because Solexa qualities should all be >= 64. Do not modify this array!
      • convertSolexaQualityCharsToPhredBinary

        public void convertSolexaQualityCharsToPhredBinary​(byte[] solexaQuals)
        Decodes an array of solexa quality ASCII chars into Phred numeric space. Decode in place in order to avoid extra object allocation.
      • convertSolexaQualityCharsToPhredChars

        public void convertSolexaQualityCharsToPhredChars​(byte[] solexaQuals)
        Decodes an array of solexa quality ASCII chars into Phred ASCII space. Decode in place in order to avoid extra object allocation.
      • convertSolexa_1_3_QualityCharsToPhredBinary

        public void convertSolexa_1_3_QualityCharsToPhredBinary​(byte[] solexaQuals)
        Casava 1.3 stores phred-scaled qualities, but non-standard because they have 64 added to them rather than the standard 33.
        Parameters:
        solexaQuals - qualities are converted in place.
      • convertSolexa_1_3_QualityCharsToPhredBinary

        public void convertSolexa_1_3_QualityCharsToPhredBinary​(int offset,
                                                                int length,
                                                                byte[] solexaQuals)