doc on read geometry

[rob-p]

From the alevin-fry repo (by @fransua)

Hi,
I cannot find clear help on read_geometry. There are a couple of examples but they do not seem to work for me and I am struggling to change them.
Specifically I have several questions:

what does the "read_geometry" refers to? I saw that it is usually set to "2[1-end]", but why only read 2, and when does the whole read is not a read?

what is the pattern of inclusion exclusion? 1-10 starts at the first nucleotide but includes the ninth or the tenth too?

How does alevin-fry deals with unexact position, for instance in my case the cell tag can start anywhere between position 85 and 115 because of a variable polyA before.

thanks

[rob-p]

Regarding the last point, cc @Gaura. Regarding a description of the read geometry, it can be found in the release notes for salmon 1.4.0 here. Though, we should certainly add something to the full docs.

[Gaura]

Yes, finishing up #734 would be additionally helpful.