Method: SSW::Align#ref_begin1

Defined in:
lib/ssw/align.rb

#ref_begin1 ⇒ Integer

Returns 0-based best alignment beginning position on reference; ref_begin1 = -1 when the best alignment beginning position is not available.

Returns:

  • (Integer) —

    0-based best alignment beginning position on reference; ref_begin1 = -1 when the best alignment beginning position is not available



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = LibSSW::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end