Option to ignore synonymous mutations

[rzelle-lallemand]

In our testing of ChroQueTas v1.0.0 (conda), we noticed that hits are reported for synonymous mutations in the FungAMR dataset. An example below, where the reference S288C genome of Saccharomyces cerevisiae (from http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/ ) shows a hit for N832N in the HAP1 gene:

ChroQueTas.sh -g saccharomyces_cerevisiae_R64-5-1_20240529.fasta -o test -s Saccharomyces_cerevisiae

Could ChroQueTas please be changed to either ignore synonymous mutations by default, or have an option to ignore them? For our needs we would like to avoid false-positives.

It also looks like the FungAMR database (https://github.com/Landrylab/FungAMR/blob/69e3805eded6fafd4ae904ff9b2417e4778f8299/FungAMR_070425.csv) currently doesn't store the nucleotide changes that caused AMR resistance for synonymous mutations, which makes it harder to check whether these are false-positives or true-positives.

I found at least two more synonymous mutations in the FungAMR database: Candida albicans Fsk1 S645S, and Botrytis cinerea SdhB I274I.