Hi Pierre, I just noticed that snpeff upstream has tagged a new release. I've injected the new tarball into Salsa Git but did not yet worked on the quilt patches that need to be adapted. If you throw an ENOTIME error I could see how far I might come with the changes. If you find some spare time for this issue I'd leave further changes to you.
Kind regards Andreas. -- http://fam-tille.de