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

Bio::Sequence::QualityScore::Phred is a module having quality calculation methods for the PHRED quality score.

BioRuby internal use only (mainly from Bio::Fastq).

Methods

Included Modules

Converter

External Aliases

convert_nothing -> convert_scores_from_phred
convert_nothing -> convert_scores_to_phred
convert_scores_from_solexa_to_phred -> convert_scores_from_solexa
convert_scores_from_phred_to_solexa -> convert_scores_to_solexa

Public Instance methods

p2q(probabilities)

Alias for phred_p2q

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

[Source]

     # File lib/bio/sequence/quality_score.rb, line 119
119:       def phred_p2q(probabilities)
120:         probabilities.collect do |p|
121:           p = Float::MIN if p < Float::MIN
122:           q = -10 * Math.log10(p)
123:           q.finite? ? q.round : q
124:         end
125:       end

PHRED score to probability conversion.


Arguments:

  • (required) scores: (Array containing Integer) scores
Returns:(Array containing Float) probabilities (0<=p<=1)

[Source]

     # File lib/bio/sequence/quality_score.rb, line 96
 96:       def phred_q2p(scores)
 97:         scores.collect do |q|
 98:           r = 10 ** (- q / 10.0)
 99:           if r > 1.0 then
100:             r = 1.0
101:           #elsif r < 0.0 then
102:           #  r = 0.0
103:           end
104:           r
105:         end
106:       end
q2p(scores)

Alias for phred_q2p

Type of quality scores.


Returns:(Symbol) the type of quality score.

[Source]

    # File lib/bio/sequence/quality_score.rb, line 87
87:       def quality_score_type
88:         :phred
89:       end

[Validate]