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).
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 |
Probability to PHRED score conversion.
The values may be truncated or incorrect if overflows/underflows occurred during the calculation.
Arguments:
Returns: | (Array containing Float) scores |
# 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:
Returns: | (Array containing Float) probabilities (0<=p<=1) |
# 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