1f3dcd25bcbefcda72218a76f0cb609460bc9b98,nucleus/examples/ascii_pileup.py,,main,#,45

Before Change

  r = ranges.parse_literal(argv[2])
  position = r.start

  with sam.SamReader(in_sam) as sam_reader:
    reads = sam_reader.query(r)
    pos_seq_pairs = sorted(
        (read.alignment.position.position, read.aligned_sequence)
        for read in reads)
    if not pos_seq_pairs:
      print("No overlapping reads found for", argv[2])
      sys.exit(0)

    left_position = pos_seq_pairs[0][0]
    for start, seq in pos_seq_pairs:
      print_read(left_position, start, position, seq)


if __name__ == "__main__":
  app.run(main)

After Change

    return -1
  in_sam = argv[1]
  query = argv[2]
  print("\n".join(ascii_pileup(in_sam, query)))


if __name__ == "__main__":
  app.run(main)

Instances