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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
44 stars 6 forks source link

OLOGRAM: exclusive combinations #157

Closed dputhier closed 3 years ago

dputhier commented 3 years ago

Hi @qferre, I dont understand why setting -mocs to --more-bed +1 give exact combination (I guess this is length(--more-bed) + 1). If reference regions are A,B,C I could be interested in query+X+Y in exact mode but not query+X+Y+Z. My feeling is that a second argument controlling exact/inexact would be required. But there is maybe something I missed...

qferre commented 3 years ago

Hi Denis,

You are right, there is not good reason why this is so. It is an artifact of the way I implemented exact and inexact counting in the code, it was simpler to write the arguments like this at the time.

I should give a separate argument for exact and inexact. I'll get on it as soon as I can.

qferre commented 3 years ago

Working on it right now. I am making some more backend changes (exposing additional parameters in MODL's API) and I'll push it along with the rest, once all the unitary tests pass.

qferre commented 3 years ago

Fixed in 2731a7fe471801d377b6ccf0faa6fb856d12484d.