docs: def get_SAM(self,min_intron_size=68):
      """Get a SAM object representation of the alignment.
  
      :returns: SAM representation
      :rtype: SAM
  
      """
      from seqtools.format.sam import SAM
      #ar is target then query
      qname = self.alignment_ranges[0][1].chr
      flag = 0
      if self.strand == '-': flag = 16
      rname = self.alignment_ranges[0][0].chr
      pos = self.alignment_ranges[0][0].start
      mapq = 255
      cigar = self.construct_cigar(min_intron_size)
      rnext = '*'
      pnext = 0
      tlen = 0 # possible to set if we have a reference
      if self._options.reference:
         if rname in self._options.reference: 
            tlen = len(self._options.reference[rname])
      seq = self.query_sequence
      if not seq: seq = '*'
      qual = self.query_quality
      if not qual: qual = '*'
      #seq = '*'
      #qual = '*'
      if self.strand == '-':
        seq = rc(seq)
        qual = qual[::-1]
      ln = qname + "\t" + str(flag) + "\t" + rname + "\t" + \
           str(pos) + "\t" + str(mapq) + "\t" + cigar + "\t" + \
           rnext + "\t" + str(pnext) + "\t" + str(tlen) + "\t" + \
           seq + "\t" + qual
      return SAM(ln,reference=self._reference)