Module Bio::Sequence::QualityScore::Converter
In: lib/bio/sequence/quality_score.rb

Converter methods between PHRED and Solexa quality scores.

Methods

Public Instance methods

Does nothing and simply returns the given argument.


Arguments:

  • (required) scores: (Array containing Integer) quality scores
Returns:(Array containing Integer) quality scores

[Source]

    # File lib/bio/sequence/quality_score.rb, line 72
72:       def convert_nothing(scores)
73:         scores
74:       end

Converts PHRED scores to Solexa scores.

The values may be truncated or incorrect if overflows/underflows occurred during the calculation.


Arguments:

  • (required) scores: (Array containing Integer) quality scores
Returns:(Array containing Integer) quality scores

[Source]

    # File lib/bio/sequence/quality_score.rb, line 40
40:       def convert_scores_from_phred_to_solexa(scores)
41:         sc = scores.collect do |q|
42:           t = 10 ** (q / 10.0) - 1
43:           t = Float::MIN if t < Float::MIN
44:           r = 10 * Math.log10(t)
45:           r.finite? ? r.round : r
46:         end
47:         sc
48:       end

Converts Solexa scores to PHRED scores.

The values may be truncated if overflows/underflows occurred during the calculation.


Arguments:

  • (required) scores: (Array containing Integer) quality scores
Returns:(Array containing Integer) quality scores

[Source]

    # File lib/bio/sequence/quality_score.rb, line 58
58:       def convert_scores_from_solexa_to_phred(scores)
59:         sc = scores.collect do |q|
60:           r = 10 * Math.log10(10 ** (q / 10.0) + 1)
61:           r.finite? ? r.round : r
62:         end
63:         sc
64:       end

[Validate]