Set double recombinants with to missing with maskTransitionSites()
(e.g. in
the sequence HHAABB, AA is replaced by missing data, NN), and set erroneous
calls at the start and end of chromosomes to missing with
maskChromosomeEnds()
(e.g. in the chromosome start sequence of 5'-AAHH or
end sequence BBAA-3', both AAs are replaced by NN).
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