Further improve selection of best epitope in aggregate report

[susannasiebert]

From #870 (comment) (credit @toddajohnson):

I was wondering about the impact of pVACtools's TSL filter last week, so I summarized genes in the Gencode build 38 (ENSEMBL 104) gtf for min. and max. TSL as well as if transcripts were labeled with other annotations used by Ensembl to prioritize gene models such as MANE, CCDS, etc.. Of 19670 protein-coding genes, 1043 only had transcripts with tslNA. From reviewing those tslNA only genes and Ensembl's TSL description, it looks to me like excluding tslNA would remove every single-exon gene. Of course, those may be small by size, but is that really the desired behavior? Also, by excluding tslNA and setting a default to TSL<=1 (while including tx. with no TSL annotation) would remove about 3000 (15%) of protein-coding genes. It seems that setting the ability to annotate using other Ensembl flags like MANE, APPRIS, Ensemble canonical, etc. might be more robust.