Bwa Gapped Alignment

Question

[Bioscientist]

bwa aln has the option "-o INT Maximum number of gap opens [1] " Does this mean by default maximum only 1 gap is allowed?

However, I ran BWA by default and I can see lots of my alignment includes say 5bp, 10bp gaps. How to explain this?

thx

Answer 1

[Manu Prestat]

I guess that you can have a single gap of length 10pb. This is still one gap.

[Bioscientist]

ok, i see..One gap can contain many bases....actually my gap can include 20bp as far as I see.