This is implemented in Rcpp for speed. It is designed to read a single replicate coalescent simulation in macs' msformatter format and convert the 0/1's to 1/2's and return in a big integer matrix of haplotypes that can then be put together as desired later. (i.e. different pops and into different diploid individuals)
the path to the mac | msformatter output file to read in. Note that tilde expansion will not occur on this path
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