Handling missing SNPs (extract_snpvar.py)

[bschilder]

extract_snpvar.py

Currently, when Not all SNPs in the SNPs file were found in the meta file. Wrote a list of missing SNPs appears, it registers as an error and stops the script. In my fork I modified this so that it simply removes the missing SNPs and continues (lines 99-102).

[omerwe]

Thanks Brian! I prefer to keep the default behavior so that users can't miss the omission of some SNPs, but I added a flag called --allow-missing which does what you suggest.

[bschilder]

I see, thanks!