code: def _get_fastq_in_region(region, align_bam, out_base):
      
      out_file = "{0}.fastq".format(out_base)
      if not file_exists(out_file):
          with pysam.Samfile(align_bam, "rb") as in_pysam:
              with file_transaction(out_file) as tx_out_file:
                  with open(tx_out_file, "w") as out_handle:
                      contig, start, end = region
                      for read in in_pysam.fetch(contig, int(start), int(end)):
                          seq = Seq.Seq(read.seq)
                          qual = list(read.qual)
                          if read.is_reverse:
                              seq = seq.reverse_complement()
                              qual.reverse()
                          out_handle.write("@{name}\n{seq}\n+\n{qual}\n".format(
                                  name=read.qname, seq=str(seq), qual="".join(qual)))
      return out_file
docs: Retrieve fastq files in region as single end.
      Paired end is more complicated since pairs can map off the region, so focus
      on local only assembly since we've previously used paired information for mapping.