Vaxrank 1.4.0 ignores --min-alt-rna-reads lower value than default

[julia326]

I ran vaxrank 1.4.0 with a less strict threshold for RNA support (--min-alt-rna-reads 1) but that flag doesn't seem to get respected - the counts are correct in the Vaxrank report, ie it registers the variant as having enough RNA support, but the ASCII report is still missing the variant at the end. (This doesn't happen with older Vaxrank versions like 1.0.0)

[iskandr]

New version of Vaxrank under dev but not yet passing tests. Sorry it's a slow WIP!