module Bio::Sequence::QualityScore::Solexa
Bio::Sequence::QualityScore::Solexa is a module having quality calculation methods for the Solexa quality score.
BioRuby internal use only (mainly from Bio::Fastq).
Public Class Methods
Public Instance Methods
Source
# File lib/bio/sequence/quality_score.rb 152 def quality_score_type 153 :solexa 154 end
Type of quality scores.
- Returns
-
(Symbol) the type of quality score.
Source
# File lib/bio/sequence/quality_score.rb 182 def solexa_p2q(probabilities) 183 probabilities.collect do |p| 184 t = p / (1.0 - p) 185 t = Float::MIN if t < Float::MIN 186 q = -10 * Math.log10(t) 187 q.finite? ? q.round : q 188 end 189 end
Probability to Solexa score conversion.
Arguments:
-
(required) probabilities: (Array containing Float) probabilities
- Returns
-
(Array containing Float) scores
Also aliased as: p2q
Source
# File lib/bio/sequence/quality_score.rb 161 def solexa_q2p(scores) 162 scores.collect do |q| 163 t = 10 ** (- q / 10.0) 164 t /= (1.0 + t) 165 if t > 1.0 then 166 t = 1.0 167 #elsif t < 0.0 then 168 # t = 0.0 169 end 170 t 171 end 172 end
Solexa score to probability conversion.
Arguments:
-
(required) scores: (Array containing Integer) scores
- Returns
-
(Array containing Float) probabilities
Also aliased as: q2p