Modified bitwise.pgen to produce more meaningful data.

bitwise.pgen now calculates pgen values in 8 pair groups across all samples.
bitwise.pgen now returns a matrix representing each group in each sample.
Both bitwise.pgen and bitwise.dist now sanitize genlight objects to ensure they have data for all chromosomes.
This prevents a rare crash caused by a SNPbin object of ploidy 2 or higher containing only 1 chromosome of data.