Bio::Sequence::QualityScore::Solexa is a module having quality calculation methods for the Solexa quality score.
BioRuby internal use only (mainly from Bio::Fastq).
Type of quality scores.
Returns |
(Symbol) the type of quality score. |
# File lib/bio/sequence/quality_score.rb, line 152 def quality_score_type :solexa end
Probability to Solexa score conversion.
Arguments:
(required) probabilities: (Array containing Float) probabilities
Returns |
(Array containing Float) scores |
# File lib/bio/sequence/quality_score.rb, line 182 def solexa_p2q(probabilities) probabilities.collect do |p| t = p / (1.0 - p) t = Float::MIN if t < Float::MIN q = -10 * Math.log10(t) q.finite? ? q.round : q end end
Solexa score to probability conversion.
Arguments:
(required) scores: (Array containing Integer) scores
Returns |
(Array containing Float) probabilities |
# File lib/bio/sequence/quality_score.rb, line 161 def solexa_q2p(scores) scores.collect do |q| t = 10 ** (- q / 10.0) t /= (1.0 + t) if t > 1.0 then t = 1.0 #elsif t < 0.0 then # t = 0.0 end t end end
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