module Bio::Sequence::QualityScore::Converter

Converter methods between PHRED and Solexa quality scores.

Public Instance Methods

convert_nothing(scores) click to toggle source

Does nothing and simply returns the given argument.

Arguments:

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

Returns: (Array containing Integer) quality scores

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

convert_scores_from_phred_to_solexa(scores) click to toggle source

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

   # File lib/bio/sequence/quality_score.rb
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

convert_scores_from_solexa_to_phred(scores) click to toggle source

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

   # File lib/bio/sequence/quality_score.rb
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