Fixing "Found overlap between homozygous and heterozygous CpG sites" error

[Christopher-Peterson]

I'm getting the error "Found overlap between homozygous and heterozygous CpG sites. Check FASTA file is masked" when I try to use CpelAsm, and I'm trying to figure out which part of my input is causing it. I looked at the relevant part of the source code, but I'm new to Julia and wasn't able to glean much.

What exactly is the overlap referring to; is it a feature of the VCF file, the BAMs, or an interaction of them?

My input files are the N-masked genome fasta and three BAMs (genome1, genome2, unassigned) created by SNPsplit plus a VCF file. The VCF is derived from the file that I used to N-mask the genome and prepare the SNP list for SNPsplit, but I modified it to follow the VCF in the example (e.g., combining two 1/1 and 0/0 samples into one 1/0 sample and adding the haplotype tag).

Thank you for your time.