gistfile1.rb

model Intersect
  def self.intersect_streams_read(io, sep=":")
    line = io.gets.strip
    parts = line.split(sep)
    chr, start, eend, *rest = parts
    [line,chr, start.to_i, eend.to_i, rest]
  end

  def self.intersect_streams(f1, f2, out, sep=":")
    finish = false
    line1, chr1, start1, eend1, rest1 = intersect_streams_read(f1,sep)
    line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep)
    while not finish
      case chr1 <=> chr2
      when -1
        move = 1
      when 1
        move = 2
      else
        if eend1 < start2
          move = 1
        elsif eend2 < start1
          move = 2
        else
          pos2 = f2.pos

          sline2, schr2, sstart2, seend2, srest2 = line2, chr2, start2, eend2, rest2
          while chr1 == chr2 and ((start1 <= eend2 and eend1 >= start2)) 
            out.puts line1 + "\t" + line2
            if f2.eof?
              chr2 = 'next2'
            else
              line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep)
            end
          end
          line2, chr2, start2, eend2, rest2 = sline2, schr2, sstart2, seend2, srest2 
          f2.seek(pos2)
          move = 1
        end
      end

      case move
      when 1
        if f1.eof?
          finish = true
        else
          line1, chr1, start1, eend1, rest1 = intersect_streams_read(f1,sep)
        end
      when 2
        if f2.eof?
          finish = true
        else
          line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep)
        end
      end
    end
  end
end