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FOI-Bioinformatics / CanSNPer2

CanSNPer2: A toolkit for SNP-typing bacterial genomes.
GNU General Public License v3.0
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fixed unintented break of loop and input checking for duplicate positions #38

Closed jaclew closed 9 months ago

jaclew commented 10 months ago

I made a database with added custom SNPs that were not called as expected. I identified the bug to be due to a presumably unintented break in the loop that iterates SNPs in each alignment.

jaclew commented 9 months ago

I added a commit with input-checking of SNPs. It checks if there are multiple SNPs reported at the same position. When working with a workflow that automatically discovers novel CanSNPs, I sometimes had a SNP-candidates reported by two (or more) subclades which caused the program to hang (multiprocessing stalled at .join() for CanSNPer2.py in function find_snps_multiproc). Obviously, such SNPs are not desired. Still, it is helpful if CanSNPer2 can tell when an input is not compatible.