What is the --tip-size used for?

[ruoyu1123]

In contact_map, there is a param named tip-size I cant understand. its value is initialized none and is not input value. But in count_sites, it is used to partition the seq. So could you tell me the means of param ?

[cerebis]

Hi @ruoyu1123 , sorry for taking so long to reply!

--tip-size pertains to a downstream operation that was removed from bin3C and should probably be removed from the UI at this point.

It was used to construct particular type of contact map that was then used to scaffold (order and orientate) contigs. The approach was to convert Hi-C contacts into a traveling salesman problem. I had some success with this idea, but it was not consistent enough to be released in general. The scaffolding operation was moved to a separate program (repo) called scaffold3C, but this tool has never been published or sufficiently validated, sitting idle for a few years now.