--EDIT-- For a corrected review see next answer below
I had difficulties to retrieve the meaning of R in a cigar string from the annotation pipeline MAKER.
Looking around on internet I realised how confused was the information related to the CIGAR format. Different toosl use different
Here is the most shared and known one, the one related to the sam format:
I'm using Exonerate and here is its CIGAR format:
--EDIT-- THIS is not CIGAR but VULGAR format
Still no R... so (Helped by the MAKER developer) I finally found an old resource from FlyBase described the CIGAR format like that:
So, in order to gather all the information in one place I did a union of the different operators and end-up with this last table, hoping it would help some lost souls like I was:
--EDIT-- THIS table contains VULGAR format operators and the H from the CIGAR format is missing
I haven't checked carefully if some definitions can be contradictory (e.g for F and I), so any comment or correction is very welcome.