FindPaths genetic map

[lynnjo]

This is a suggestion from Jeff Ross-Ibara. I am quoting from a slack message:

we're seeing lots of haplotype switching in centromeric regions. probably bad mapping, but also seems odd to have a single recombination rate genome-wide, since the observed rate varies across two orders of magnitude. would it be hard to add a look-up table such that we could give a genetic map and based on the map the PHG decides on the rec rate to use?

This is just to replace the current --prob-same-gamete with a vector so that each ref range has a different probability based on the genetic map.

Which could just be looked up from a table

I supply a genetic map with bp and cm. Internally you use a spline or something to approximate the cm for reference range start and end. Then the cm size of the ref range gives you the --prob-same-gamete for that range.

I've attached an example table.
ZeaSynDH_Trial1100_acc0.9_combinedContiguous_Chr1_inCM_plot.pdf