pileup consolidation tool

Question

[joe]

Hello Biostars,

I'm looking for a pileup tool that will consolidate output to a table that is strand sensitive, separates +/-, includes indels as well count of starts and stops. I'm familiar with many tools, but it seems like none of them are able to capture everything listed. JACUSA2 is the closest I've found but this doesn't have al the features. I've included an example header below for what I'm after. Thanks!

chr loc ref strand  A   T   C   G   a   t   c   g   Insertion   Deletion    Stops   Starts
1   888659  T   +   0   9   0   2   0   0   0   0   2:AG|1:AGAG 1:ATT   3   2

[Pierre Lindenbaum]

what is the scientific question you're trying to answer ?

[joe]

Detection of RNA modifications.

[joe]

I tried to use Rsamtools::pileup() but haven't been able to come up with the right parameters to pass in PileupParam ...maybe somewhere here knows better?