Method: Bio::MAF::MAFParsing#parse_block_data

Defined in:
lib/bio/maf/parser.rb

#parse_block_data ⇒ Block

Parse a Block from the current position. Requires that #s and #chunk_start be set correctly.

Returns:

  • (Block) —

    the alignment block.



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# File 'lib/bio/maf/parser.rb', line 298

def parse_block_data
  block_start_pos = s.pos
  block_offset = chunk_start + block_start_pos
  s.scan(/^a\s*/) || parse_error("bad a line")
  block_vars = parse_maf_vars()
  seqs = []
  payload = s.scan_until(/^(?=a)/)
  unless payload
    payload = s.rest
    s.pos = s.string.size # jump to EOS
  end
  filtered = false
  lines = payload.split("\n")
  until lines.empty?
    line = lines.shift
    first = line.getbyte(0)
    if first == S
      seq = parse_seq_line(line, sequence_filter)
      if seq
        seqs << seq
      else
        filtered = true
      end
    elsif first == E && parse_empty
      e_seq = parse_empty_line(line, sequence_filter)
      if e_seq
        seqs << e_seq
      else
        filtered = true
      end
    elsif first == I && parse_extended
      parts = line.split
      parse_error("wrong i source #{parts[1]}!") unless seqs.last.source == parts[1]
      seqs.last.i_data = parts.slice(2..6)
    elsif first == Q && parse_extended
      _, src, quality = line.split
      parse_error("wrong q source #{src}!") unless seqs.last.source == src
      seqs.last.quality = quality
    elsif [I, E, Q, COMMENT, nil].include? first
      next
    else
      if opts[:strict]
        parse_error "unexpected line: '#{line}'"
      else
        LOG.warn "Ignoring invalid MAF line: '#{line}'"
      end
    end
  end
  b = Block.new(block_vars,
                seqs,
                block_offset,
                s.pos - block_start_pos,
                filtered)
  if opts[:retain_text]
    b.orig_text = s.string.slice(block_start_pos...(s.pos))
  end
  return b
end