pyBigWig values method does not take argument numpy=True

[tanjimin]

maxATAC/maxatac/utilities/normalization_tools.py

Line 47 in 83cd5d2

chr_vals = np.nan_to_num(input_bigwig.values(chromosome, 0, input_bigwig.chroms(chromosome), numpy=True))

  File "/gpfs/home/.conda/envs/maxatac/lib/python3.9/site-packages/maxatac/utilities/genome_tools.py", line 236, in chromosome_blacklist_mask
    return blacklist_bigwig_stream.values(chromosome,
TypeError: values() takes no keyword arguments

Same format in another file:

maxATAC/maxatac/utilities/genome_tools.py

Line 239 in 83cd5d2

numpy=True) != 1 # Convert to boolean array, select areas that are not 1

Removing numpy=True seems to resolve the issue.

[tacazares]

Hey @tanjimin,
This is a known issue, #87 and #96 (comment), that is due to the inability of pybigwig to recognize that your system has numpy installed. Try some of the suggested tips, I am not sure how removing the numpy=True fix will affect the import of values/downstream processes.
Take care,
Tareian