code: def fai_from_bam(ref_file, bam_file, out_file, data):
      
      contigs = set([x.contig for x in idxstats(bam_file, data)])
      if not utils.file_uptodate(out_file, bam_file):
          with open(ref.fasta_idx(ref_file, data["config"])) as in_handle:
              with file_transaction(data, out_file) as tx_out_file:
                  with open(tx_out_file, "w") as out_handle:
                      for line in (l for l in in_handle if l.strip()):
                          if line.split()[0] in contigs:
                              out_handle.write(line)
      return out_file
docs: Create a fai index with only contigs in the input BAM file.