Error when providing data without PL

[dovivi]

Hi, I was testing the program but I get an error when parsing data that does not contain PL (either VCF file without PL or bed format).
To check if it was my input file I tried out with the provided bed data 701_502.filter.bed and got the same error.

(base) [user@host SNPmatch]$ snpmatch parser -v -i 701_502.filter.bed -o test
2022-08-31 17:32:58,070 - snpmatch.core.parsers - INFO - running snpmatch parser!
2022-08-31 17:32:58,071 - snpmatch.core.parsers - INFO - reading the position file
2022-08-31 17:32:58,100 - snpmatch.core.parsers - INFO - creating snpmatch parser file: test.npz
2022-08-31 17:32:58,117 - root - ERROR - ufunc 'add' did not contain a loop with signature matching types (dtype('<U2'), dtype('<U2')) -> None
Traceback (most recent call last):
  File "/home/user/miniconda3/lib/python3.9/site-packages/snpmatch/__init__.py", line 177, in main
    args['func'](args)
  File "/home/user/miniconda3/lib/python3.9/site-packages/snpmatch/__init__.py", line 134, in snpmatch_parser
    parsers.potatoParser(inFile = args['inFile'], logDebug =  args['logDebug'], outFile = args['outFile'])
  File "/home/user/miniconda3/lib/python3.9/site-packages/snpmatch/core/parsers.py", line 217, in potatoParser
    inputs = ParseInputs(inFile, logDebug, outFile)
  File "/home/user/miniconda3/lib/python3.9/site-packages/snpmatch/core/parsers.py", line 86, in __init__
    self.case_interpret_inputs(outFile + ".stats.json")
  File "/home/user/miniconda3/lib/python3.9/site-packages/snpmatch/core/parsers.py", line 113, in case_interpret_inputs
    statdict["depth"] = np.nanmean(self.dp)
  File "<__array_function__ internals>", line 180, in nanmean
  File "/home/user/miniconda3/lib/python3.9/site-packages/numpy/lib/nanfunctions.py", line 1034, in nanmean
    return np.mean(arr, axis=axis, dtype=dtype, out=out, keepdims=keepdims,
  File "<__array_function__ internals>", line 180, in mean
  File "/home/user/miniconda3/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 3432, in mean
    return _methods._mean(a, axis=axis, dtype=dtype,
  File "/home/user/miniconda3/lib/python3.9/site-packages/numpy/core/_methods.py", line 180, in _mean
    ret = umr_sum(arr, axis, dtype, out, keepdims, where=where)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'add' did not contain a loop with signature matching types (dtype('<U2'), dtype('<U2')) -> None

Just to remark: when I provide a VCF file with PL I do not get the error.

== Update ==
I've just found where the problem comes from:
When parsing from .bed, DPmean is set to "NA" (line but afterwards this comuted statdict["depth"] = np.nanmean(self.dp) is called, which gives the error). The same happens with VCF file, if DP is not present (or not present in INFO), it is set to a list of "NA"s, giving afterwards the same error.

[baozg]

Have you resloved this problem?