Deal with older vcf formats and samples with missing data

[eniktab]

No description provided.

[sbslee]

Hi @eniktab,

Thank you for the PR. However, I can't merge it for several reasons:

1. The target branch for this PR is master which should have been a dev branch such as 0.26.0-dev.
2. I cannot understand the motivations behind the PR. I'd greatly appreciate if you could provide more details on why you wrote the PR and what you are trying to fix/improve. That being said, in the future, I'd strongly recommend that you first open an issue at this repository before opening a PR. The same is true for another PR you wrote for one of my other packages, fuc (Deal with duplicates and different formats  fuc#76).
3. I intentionally designed PyPGx such that when there are two different sample sets, PyPGx won't allow the process to complete when calling genotypes. When this occurs, it's better for the user to go back and try to understand why his or her datasets have different sample sets, rather than blindly allowing them to move forward with only overlapping samples. This may be obvious for you but many of the PyPGx users are not too savvy in bioinformatics.

pypgx/pypgx/api/genotype.py

Lines 622 to 624 in f1dd988

	_diff = set(cnv_calls.data.index)- set(alleles.data.index)
	print(_diff)
	print("Are missing and will be droped")

4. Could you provide more details on why you had to make the changes for:

pypgx/pypgx/api/utils.py

Lines 1303 to 1306 in f1dd988

	regions = [
	item for item in regions
	if item.split(':')[0].isdigit() or item.split(':')[0] in {'X', 'Y'}
	]