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harrispopgen / mutyper

Ancestral k-mer mutation types for SNP data
https://harrispopgen.github.io/mutyper/
MIT License
7 stars 3 forks source link

Fix for ancestral subcommand compressed fasta input, extra logging info, and a snakemake #28

Closed mrvollger closed 3 years ago

mrvollger commented 3 years ago

Hey Will,

Mostly I added some things for my own debugging, but there was an issue with copying the ref to ancestral when the ref was compressed because pafaidx needed a mutable ancestral file which doesn't work with bgzip.

I also added some logging so you get warnings if more than half your data is not lifted or no variants are processed by the variants subcommand.

And finally I dropped in my snakemake workflow for mutpyer in case you want to include it in the repo with a CI test for the snakemake.

mrvollger commented 3 years ago

Removed the snakmake stuff and I added comments with mrv somewhere in them for every line I added (hope I didn't miss any). sorry about the black formatting I wasn't thinking about it.