For reversion mutations in the tree, mut_nuc is the same as ref_nuc and par_nuc is the change being reverted. matUtils mask --mask-mutations was comparing ref_nuc instead of par_nuc, so it was unable to recognize reversions specified in its input file that were present in the tree. (For mutations parsed from the input file, ref_nuc is set to the same value as par_nuc, but that is not the case for mutations in the tree.)
For reversion mutations in the tree, mut_nuc is the same as ref_nuc and par_nuc is the change being reverted.
matUtils mask --mask-mutationswas comparing ref_nuc instead of par_nuc, so it was unable to recognize reversions specified in its input file that were present in the tree. (For mutations parsed from the input file, ref_nuc is set to the same value as par_nuc, but that is not the case for mutations in the tree.)