Enable --ignore_merge_codons in ivar_variants_to_vcf when no .gff file is given

[svarona]

Description of feature

When no .gff file for annotation is given to the pipeline, the ivar_variants_to_vcf step is not performing well during the codon merging.

Also, the script should be updated in order to merge only those positions with the same allele frequency, not just keeping the first variant's allele frequency.