This should prevent any further "substructure has residue [...] which is not
in self.target" errors. Add test and doc to clarify what we ignore.

This fixes a problem where ties aren't being resolved correctly

This improves error messages when the counts line is invalid and the
calls to substr() return raw C++ errors.

comes at limited additional runtime costs

trust me, its a bit better that way...

Apply crude collision detection to avoid pairwise distance computations
between chains that are far apart.

Yolo, this code is totally untested. Xavier, please give it a try ;)