Can't open bgen using symbolic links #42
Description
Hello,
I want to use the numpy inspired API to open an bgen using a symbolic link. I want to do this because I don't want to create the .metadata2.mmm file in the shared directory where the bgen lives. I thought I recalled being able to do this in a previous version of bgen-reader, but am running into the following problem now.
from bgen_reader import open_bgen
wha = open_bgen('/n/holylfs05/LABS/liang_lab_l3/Lab/jordan/ssctpr/data/ukbb_symbolic_link/ukb_imp_chr1_v3.bgen')
Traceback (most recent call last):
File "", line 1, in
File "/n/home_fasse/jrossen/.conda/envs/ssctpr2/lib/python3.9/site-packages/bgen_reader/_bgen2.py", line 133, in init
assert_file_exist(filepath)
File "/n/home_fasse/jrossen/.conda/envs/ssctpr2/lib/python3.9/site-packages/bgen_reader/_file.py", line 14, in assert_file_exist
raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), filepath)
I don't have a very strong understanding of how PosixPath works, but after a little playing around, it seems like PosixPath precludes the use of symbolic links.
Either allowing for the use of symbolic links, or allowing the user to specify a directory where .metadata2.mmm should be created would solve my problem completely.
Thanks for making this software!