module Bio::Sequence::QualityScore::Phred
Bio::Sequence::QualityScore::Phred is a module having quality calculation methods for the PHRED quality score.
BioRuby internal use only (mainly from Bio::Fastq).
Public Class Methods
Public Instance Methods
Source
# File lib/bio/sequence/quality_score.rb 121 def phred_p2q(probabilities) 122 probabilities.collect do |p| 123 p = Float::MIN if p < Float::MIN 124 q = -10 * Math.log10(p) 125 q.finite? ? q.round : q 126 end 127 end
Probability to PHRED score conversion.
The values may be truncated or incorrect if overflows/underflows occurred during the calculation.
Arguments:
-
(required) probabilities: (Array containing Float) probabilities
- Returns
-
(Array containing Float) scores
Also aliased as: p2q
Source
# File lib/bio/sequence/quality_score.rb 98 def phred_q2p(scores) 99 scores.collect do |q| 100 r = 10 ** (- q / 10.0) 101 if r > 1.0 then 102 r = 1.0 103 #elsif r < 0.0 then 104 # r = 0.0 105 end 106 r 107 end 108 end
PHRED score to probability conversion.
Arguments:
-
(required) scores: (Array containing Integer) scores
- Returns
-
(Array containing Float) probabilities (0<=p<=1)
Also aliased as: q2p
Source
# File lib/bio/sequence/quality_score.rb 89 def quality_score_type 90 :phred 91 end
Type of quality scores.
- Returns
-
(Symbol) the type of quality score.