added gsub for to convert '?' strands to '*'

[areyesq89]

Hello,

Thanks for putting together snapcount: it makes our jobs easier to many :)

I noticed that in the most recent versions of the database, sometimes the junction's strands are reported as "?". This caused errors when converting these junctions to a GRanges objects (and subsequently, SummarizedExperiments objects.

I added a gsub to convert '?' strands to "*" before converting to GRanges objects.

Hope this is useful,
Alejandro

[ChristopherWilks]

Thanks @areyesq89

I decided to use "?"s as the new compilations (srav3h, srav1m, tcgav2, and gtexv2) have non-canonical splicing in them, where the strand is ambiguous.

This was not true with the previous, recount2-related compilations (srav2, tcga, gtex, etc...) where the strand was always set.

However, I didn't take converting to GRanges objects into consideration when I made that decision.

So your update is a nice way to handle that for the time being.

But I'll have a chat internally with the team and see long term what the best way to deal with this is before we do anything.