Stoploss confused as insert

[joaoe]

This is somewhat similar to #201 although I observed this before 201 being fixed.

Genome GRCm38, ENSMUST00000006221

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
chr11   21319856        .       T       C       123     .       .       .

The variant is located at AAG AGG (T)GA TGA CAG so the first stop codon becomes CGA (a stop loss), but the 3'UTR being translated downstream then stops immediately, because there are two consecutive stop codons (first time I see this).

The annotation is reported as

Insertion(aa_ref='', aa_ref='R')

For all practical purposes, the annotation is usable, since it gets the amino-acids right. But it should be marked as StopLoss. Therefore, I'd say this is low priority. VEP and ANNOVAR get the stoploss right (but they don't translate the 3'utr in case of stop losses; there is a VEP issue about it).