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psathyrella / partis

B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction
GNU General Public License v3.0
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Option of both lambda and kappa option for light chain annotation #209

Closed krdav closed 7 years ago

krdav commented 8 years ago

Currently partis gives the option of either lambda or kappa light chain. A good addition to that would be to add the option of both using lambda and kappa germlines for sw align and pick the best match. In many applications presumably you will not know the origin of the light chain germline before hand, and most times samples will contain both lambda and kappa VL sequences. Hence, in those cases it makes most sense to let partis decide on the fly which germline to choose from.

psathyrella commented 7 years ago

if possible, when implementing this I should make it more difficult to have a mismatch between the germline gene chain and the --chain argument (see #214).

krdav commented 7 years ago

Option is now there and it is working nicely.