Handling of temporary files by multigrmpy.py about paragraph HOT 2 CLOSED

Thanks for finding this out!
For item 1, that's a problem. I'll leave it open until we fix it.
For 2 & 3, I believe the temporary directory, if not specified by --scratch-dir, will be completely removed upon completion. Do you mean they're not cleaned when you have --scratch-dir specified?

from paragraph.

Hi Sai,

Thanks for your reply. Indeed, the temporary directory is not removed after running when explicitly setting a --scratch-dir, and neither are its contents.

Regarding issue 2, I have fixed for my purposes by adding the line 'os.remove(indexed_vcf.name + ".csi")' after line 106 in the init.py file of vcf2paragraph. However, I am not an experienced Python coder so I am not sure whether this is the proper way to do so.

I have also added some functionality for deleting the temporary json files in the --scratch-dir after running but I assume some users might not want this functionality for debugging purposes or closer inspection of the output. As to me, I do not need them because I only really care about the genotypes. I prefer to specify scratch-dir explicitly because it makes it easier to manage than using the common /scratch directory which is shared with other users on the system.

from paragraph.