Merge dev: plotting functions, bug fixes including handling of multiallelics - #2

Merged

charlesfoster merged 12 commits into

mainfrom

May 5, 2026

Commits on Mar 25, 2026

Added in logging for snakemake steps
charlesfoster
committed
bf9273f
Plotting and lofreq adjustments
charlesfoster
committed
e2c9ac6

Commits on Mar 26, 2026

Arguments refactor and plotting refinements
charlesfoster
committed
565f430
Fixing potential results duplication with some samples; made variant_qc more interpretable
charlesfoster
committed
f4a2b84
SOme new plot options added
charlesfoster
committed
9b785b1

Commits on Mar 27, 2026

Plot improvements
charlesfoster
committed
d6352e5

Commits on Apr 7, 2026

Updated plotting capabilities
charlesfoster
committed
796cb14

Commits on Apr 22, 2026

Added ability to generate consensus genomes + bug huntin

Charles Foster
authored and
Charles Foster
committed
49c40ed

Commits on May 5, 2026

Fixed treatment of low frequency multiallelics
charlesfoster
committed
a8a4585
Script lint fix
charlesfoster
committed
1fb3d8c
Fixed mypy pin to pass CI
charlesfoster
committed
7a21a7d
Fixed schema to pass CI
charlesfoster
committed
0cc7d22