Possible to set %identity of reads mapping to ref?

[appliedmicrobiologyresearch]

Hi there! I would love to use snippy for "mixed" datasets with multiple bacterial genomes in. At the moment I am getting mixed mapping to the rRNA operons. Is there a way of setting this in the bwa part (I'm not sure that --mapqual does what I want?). Or would masking the rRNA operons be a better method? Thanks!