Need help understanding the method from this paper

[antifolate]

I'm trying to somehow follow the method outlined in this paper for calling breakpoints after assembly and mapping to the reference (see Assembly and Validation). I couldn't figure out how to do the following step

Split-mappings with ≥25 bp of nonoverlap with an adjacent mapping on the contig were converted to BEDPE format

Do you know which tool can be used to do this? I thought it was BEDtools but didn't find a function for this purpose.