This is a simple program to count the average methylation of CpG
islands in intervals of reads that map to intervals in a reference.
This way, if there are expansions in the read that are contained
at the interval on the reference, the CpGs in the expansion are counted.
The result that is output is the mean and variance of CpG, as well as the
number of CpGs for each haplotype over a region.
This is a companion discussion topic for the original entry at github.com/ChaissonLab/countme/countme