Regarding #109#111
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@dpryan79 so I tried to implement #109 (also related to #86 ) and kind of failed half-way.
The option --NoMeCpG is a modification of CpG option to ignore the CGC contexts (since it conflicts with GC methylation). It works and output looks correct on IGV.
The option --GCH is supposed to be combined with --noCpG to get only GCH methylation. I tried to make it work at least in combination with --cytosine_report but the output file is always empty even if that line I added is being evaluated in the function
writeBlank. I think it need more modifications in theextractCallsfunction? But maybe there are other places where CG- context is always assumed? I am confused 😓I am just going to leave it here. Maybe you can help to make it work if you have time..
Best,
Vivek