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pangenome / smoothxg

linearize and simplify variation graphs using blocked partial order alignment
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Change on CLI on v0.7.0 #189

Closed sivico26 closed 1 year ago

sivico26 commented 1 year ago

Hi smoothxg team,

This should be a fairly small issue. Last week Depuplicato (v0.7) version was released promising great performance improvements.

Of course, I have to try that! So I submitted again a couple of big jobs I am running (using abPOA and SPOA) and I found that one died fairly quickly. When I checked, I found that I use a parameter that the CLI didn't get -S. That is when I realized that the CLI changed from Ciclico (v0.6.8) to Deduplicato (v0.7.0). The default poa algorithm changed from abPOA to SPOA (something that I remember being discussed in previous issues) and the -S flag changed to -A.

From a CLI design point of view, this makes sense to me. However, it does break backward compatibility. I do not necessarily have a problem with that, but I do think this should be communicated more clearly, ideally on the release introduction. In my case, if I had not run both jobs, probably I would not have noticed those changes, and I would be running a different POA algorithm without noticing until who knows when.

Keep up the good work! Cheers

P.S. I just noticed that the README still cites -A for debugging purposes but this clearly disappeared in the latest version, along with -B.

AndreaGuarracino commented 1 year ago

Youreright

I've update the release introduction, being also a bit more verbose.

About the README, I've fixed the -A flag, that is now -S. The debugging options are available only when smoothxg is compiled with -DPOA_DEBUG=ON.

Thank you for pointing out all these issues!