CrossSim

by Joshua Shapiro

A system for simulating genetic crosses.

The functionality is pretty basic, but it supports haploid or diploid individuals, tracking an arbitrary number of chromosomes.

Recombination is modeled either without interference, or with complete interference (one recombination event per chromosome), and all coordinates are on the genetic map.

TODO:

• Add functions to convert genetic map to physical. This can be done with judicious placement of markers, but it will become important for the next todo:
• Add possibility of mutations during the cross.