why 'center_coordinates' in read_gem(), but not in read_gef()?

[z-spider]

What is the effect of this parameter？Should we use it？

Stereopy/stereo/io/reader.py

Lines 1161 to 1170 in c230d6f

	def read_gef(
	file_path: str,
	bin_type: str = "bins",
	bin_size: int = 100,
	is_sparse: bool = True,
	gene_list: Optional[list] = None,
	region: Optional[list] = None,
	gene_name_index: Optional[bool] = False,
	num_threads: int = -1
	):

Stereopy/stereo/io/reader.py

Lines 45 to 53 in c230d6f

	def read_gem(
	file_path: str,
	sep: str = '\t',
	bin_type: str = "bins",
	bin_size: int = 100,
	is_sparse: bool = True,
	center_coordinates: bool = False,
	gene_name_index: bool = False
	):

Thanks for any reply！

[tanliwei-coder]

center_coordinates is only available for bins bin_type, each bin actually is a square, setting it to True means the central coordinate of each bin is set as its coordinate, otherwise, the upper left corner coordintates are used, due to some unknown historical reasons, previously, if input file is a GEM, the coordinates of bins were forced to be the center of bins, but if a GEF, bins coordinates are always the upper left corner coordintates, in order to unify the GEM and GEF, we added the parameter center_coordinates to read_gem and set it to False by default so that the bins coordinates can be the upper left corner of bins and if a user wants it to be the bin center, center_coordinates can be set to True.