Finding a map between observed bases and positions in the reference genome

[biojulia]

Finding a map between observed bases and positions in the reference genome

[kescobo]

As a first pass, I'd look here and set up the for record in reader... bit. As for what happens inside the loop, the easiest (though not necessarily most performant) thing would probably be to just make a couple of vectors and push! to them. Eg

startstops = []
refpos = []
for record  in reader
    # whatever to get start / end positions...
    push!(startstops, (starts, stops))
    push!(refpos, (position(record), rightposition(record)))
end

[scikal]

Thank you for the prompt response.

I'm trying to deal with the case of a read that contains short deletions, so the read length is smaller than the rightposition(record)-position(record).

[scikal]

I was wondering if there is a more easy solution than parsing the cigar.

[kescobo]

Ah, that I don't know. Will have to wait for someone more familiar with the format to weigh in, sorry.