class Bio::Fastq::FormatData

Bio::Fastq::FormatData is a data class to store Fastq format parameters and quality calculation methods. Bio::Fastq internal use only.

Constants

NAME: Format name. Should be redefined in subclass.
OFFSET: Offset. Should be redefined in subclass.
SCORE_RANGE: Range of score. Should be redefined in subclass. The range must not exclude end value, i.e. it must be X..Y, and must not be X…Y.

Attributes

name[R]

Format name

offset[R]

Offset when converting a score to a character

quality_score_type[R]

Type of quality scores. Maybe one of :phred or :solexa.

score_range[R]

Allowed range of a score value

symbol[R]

Format name symbol. Note that “-” in the format name is substituted to “_” because “-” in a symbol is relatively difficult to handle.

Public Class Methods

new() click to toggle source

   # File lib/bio/db/fastq.rb
52 def initialize
53   @name = self.class::NAME
54   @symbol = @name.gsub(/\-/, '_').to_sym
55   @offset = self.class::OFFSET
56   @score_range = self.class::SCORE_RANGE
57 end

Public Instance Methods

scores2str(a) { |i| ... } click to toggle source

Converts scores to a string. Overflow/underflow checks will be performed. If a block is given, when overflow/underflow detected, the score value is passed to the block, and uses returned value as the score. If no blocks, silently truncated.

Arguments:

(required) a: (Array containing Integer) score values

Returns: (String) quality string

    # File lib/bio/db/fastq.rb
 98 def scores2str(a)
 99   if block_given? then
100     tmp = a.collect do |i|
101       i = yield(i) unless @score_range.include?(i)
102       i + @offset
103     end
104   else
105     min = @score_range.begin
106     max = @score_range.end
107     tmp = a.collect do |i|
108       if i < min then
109         i = min
110       elsif i > max then
111         i = max
112       end
113       i + @offset
114     end
115   end
116   tmp.pack('C*')
117 end

str2scores(str) click to toggle source

Converts quality string to scores. No overflow/underflow checks will be performed.

Arguments:

(required) c: (String) quality string

Returns: (Array containing Integer) score values

   # File lib/bio/db/fastq.rb
82 def str2scores(str)
83   a = str.unpack('C*')
84   a.collect! { |i| i - @offset }
85   a
86 end