Bug fixed in the methyl_call_processor to better handle multi-mapped/supp reads.
This bug affected methylation call files with supp/multi-mapped reads from methylation callers that call methylation for all the mappings of a read and then go to the next read, including megalodon and DeepSignal, rather than calling based on the sorted coordinates from a bam file.
DeepSignal uses Tombo and it seems Tombo does not use supp/multi-mapping reads. Megalodon also does not use supp/multi-mappings by default. Therefore, this bug mostly affected megalodon methylation calls when the option to call methylation for supplementary reads was selected during methylation calling.