How to set up the preprocessing part of the chromosome

[qiqi277]

Hello, thank you very much for developing the Monopogen software. I have encountered some problems in the running process. I run the pig sample, but when I run the preprocessing part, it shows an error because I can't find chromosome 19. What can I do to make it work with only the first 18 chromosomes? Here is my error message.

`multiprocessing.pool.RemoteTraceback: 
Traceback (most recent call last):
  File "/public/home/zhangqiqi02/miniconda3/envs/momopogen2_env/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/public/home/zhangqiqi02/miniconda3/envs/momopogen2_env/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/public/home/zhangqiqi02/software/Monopogen/src/germline.py", line 200, in BamFilter
    for s in infile.fetch(search_chr):
  File "pysam/libcalignmentfile.pyx", line 1092, in pysam.libcalignmentfile.AlignmentFile.fetch
  File "pysam/libchtslib.pyx", line 683, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid contig `19`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/public/home/zhangqiqi02/software/Monopogen/src/Monopogen.py", line 340, in <module>
    main()
  File "/public/home/zhangqiqi02/software/Monopogen/src/Monopogen.py", line 333, in main
    args.func(args)
  File "/public/home/zhangqiqi02/software/Monopogen/src/Monopogen.py", line 221, in preProcess
    result = pool.map(BamFilter, para_lst)
  File "/public/home/zhangqiqi02/miniconda3/envs/momopogen2_env/lib/python3.9/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/public/home/zhangqiqi02/miniconda3/envs/momopogen2_env/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
ValueError: invalid contig `19`

` Looking forward to your reply!