Make pruning optional for NGSrelate and enable allele frequency based coefficients

[zjnolen]

Allow user to decide if pruning is desired for NGSrelate, but keep it on by default as it assumes independence.

Right now, the allele frequency based metrics don't work because we don't provide allele frequencies. Add an option to do this. Doing this also makes an easy way to expose the allele frequency outputs as requestable outputs instead of by products of other analyses as they are now.

[zjnolen]

Pruning now optional, allele frequency metrics will take a bit more time and will be in the next version.