Method: BioDSL::Assemble#match

Defined in:
lib/BioDSL/seq/assemble.rb

#match ⇒ Object

Method to locate overlapping matches between two sequences.



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# File 'lib/BioDSL/seq/assemble.rb', line 82

def match
  calc_overlap
  diff = calc_diff

  @offset1 = @entry1.length - @overlap - diff

  while @overlap >= @options[:overlap_min]
    mismatches_max = (@overlap * @options[:mismatches_max] * 0.01).round

    if (mismatches = match_C(@entry1.seq, @entry2.seq, @offset1, @offset2,
                             @overlap, mismatches_max)) && mismatches >= 0
      entry_merged          = entry_left + entry_overlap + entry_right
      entry_merged.seq_name = @entry1.seq_name +
        ":overlap=#{@overlap}:hamming=#{mismatches}" if @entry1.seq_name

      return entry_merged
    end

    diff > 0 ? diff -= 1 : @overlap -= 1

    @offset1 += 1
  end
end