docs: def get_alignment_strings(self,min_intron_size=68):
      """Process the alignment to get information like
         the alignment strings for each exon. These strings are used by the pretty print.
  
      :returns: String representation of the alignment in an easy to read format
      :rtype: string
      """
      qseq = self.query_sequence
      if not qseq:
        sys.exit("ERROR: Query sequence must be accessable to get alignment strings\n")
        sys.exit()
      ref = self._options.reference
      qual = self.query_quality
      if not qual: 
        qual = 'I'*len(qseq) # for a placeholder quality
      if self.strand == '-': 
        qseq = rc(qseq)
        qual = qual[::-1]
      tarr = []
      qarr = []
      yarr = []
      tdone = ''
      qdone = ''
      ydone = '' #query quality
      for i in range(len(self.alignment_ranges)):
        [t,q] = self.alignment_ranges[i]
        textra = ''
        qextra = ''
        yextra = ''
        if i >= 1:
          dift = t.start-self.alignment_ranges[i-1][0].end-1
          difq = q.start-self.alignment_ranges[i-1][1].end-1
          if dift < min_intron_size:
            if dift > 0:
              textra = str(ref[t.chr][t.start-dift-1:t.start-1]).upper()
              qextra = '-'*dift
              yextra = '\0'*dift
            elif difq > 0:
              textra = '-'*difq
              qextra = qseq[q.start-difq-1:q.start-1].upper()
              yextra = qual[q.start-difq-1:q.start-1]
          else:
            tarr.append(tdone)
            qarr.append(qdone)
            yarr.append(ydone)
            tdone = ''
            qdone = ''
            ydone = ''
        tdone += textra+str(ref[t.chr][t.start-1:t.end]).upper()
        qdone += qextra+qseq[q.start-1:q.end].upper()
        ydone += yextra+qual[q.start-1:q.end]
      if len(tdone) > 0: 
        tarr.append(tdone)
        qarr.append(qdone)
        yarr.append(ydone)
      if self.query_quality == '*': yarr = [x.replace('I',' ') for x in yarr]
      #query, target, query_quality
      return [qarr,tarr,yarr]