In Gene.R line 183-187, it looks like getSegment automatically strips the D from any name ie IGKV3D-11 == IGKV3-11. These are unique V genes I think, and this is the default (this is then used in getGene, getGene is used as a default in distToNearest). In changeo, the D is not stripped, i.e. one way in which the cloning in DefineClones.py differs from that in shazam.
Issue #50 invalid