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 input bam must be phased with HP tags. 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.

The output columns are: 1-3 chrom start end (from bed flie) 4-7 hap1: nReads avgReadLen avgCpGCount avgMeth 8-11 hap2: nReads avgReadLen avgCpGCount avgMeth

The nreads are the number of reads from the corresponding haplotype that overlap the interval, and avgReadLen is the length of each read between the bases that are mapped to the starting and ending positions of the interval. This should roughly equal the starting and ending positions of the interval. The avgCpG count is according to the read itself rather than the genome, and the avgMeth is the average of the methylation scores for all CpG islands for all reads from a haplotype.