Class: Quality

Inherits:

String

• Object
• String
• Quality

Defined in:

lib/parse_fasta/quality.rb

Overview

Provide some methods for dealing with common tasks regarding quality strings.

Instance Method Summary

• #mean_qual ⇒ Float

  Returns the mean quality for the record.

• #qual_scores ⇒ Array<Fixnum>

  Returns an array of illumina style quality scores.

Instance Method Details

#mean_qual ⇒ Float

Returns the mean quality for the record. This will be a good deal faster than getting the average with qual_scores and reduce.

Examples:

Get mean quality score for a record

Quality.new("!+5?I").mean_qual #=> 20.0

Returns:

• (Float) —

  Mean quality score for record

# File 'lib/parse_fasta/quality.rb', line 29

def mean_qual
  (self.sum - (self.length * 33)) / self.length.to_f
end

#qual_scores ⇒ Array<Fixnum>

Returns an array of illumina style quality scores. The quality scores generated will be Phred+33 (i.e., new Illumina).

Examples:

Get quality score array of a Quality

Quality.new("!+5?I").qual_scores #=> [0, 10, 20, 30, 40]

Returns:

• (Array<Fixnum>) —

  the quality scores

# File 'lib/parse_fasta/quality.rb', line 40

def qual_scores
  self.each_byte.map { |b| b - 33 }
end