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TODO.md

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Things to do:

  • test the inference in detail

  • add more tests

  • Potential insertion in V/J alignment: find a good way to deal with this [remove the sequence from the inference if the insertion overlap with the delv range]

  • test the restricted V gene option for generation.

  • modify the way I deal with added error (make it cleaner, with a "ErrorDistribution" thing or smt)

  • deal with amino-acid and generic "undefined" stuff. Strat: define an extended Dna object that the alignment can deal with + define the insertion thing so that it can deal with that This second one is slightly a pain (the first one too ? No it's fine, just a bit longer to deal with). I would need to add sums here and there, nothing impossible, but slightly more a pain. In short some position must be linked, this will complexify quite a bit the definition of Dna (more precisely this will be a new class). So UndefinedDna would contains for each position a vec/array of bytes and a int giving the positions they're connected with (just need two options for everything). This is very specific to the aa case, but why should I care. A bit complicated rn, leaving it for later.

  • clean up gen event / static event if possible.

  • add some checks so that people don't mix up the V and J files

  • allow restricted models (P(V) P(DJ))

  • allow to fix number of cores used (rayon::ThreadPoolBuilder::new().num_threads(4).build_global().unwrap(); -> make a function set_nb_threads(nb))

  • I should probably change the way I'm doing the inference (the feature object should contains ref to other features ?)

  • Could there be a problem with the D gene distribution ?

  • righor-py, better "load_model" function

  • problem in the CDR3 generation

Before version change checklist:

  • is righor-py using the cargo package or the local version ?
  • did you change the version number everywhere ?