A question about Allele.ctg.table

[YuChrming]

Dear Aouthr! For now, allhic is the closest software for success to polyploidy in which I used.But I have a bewilderment. When I use Allele.ctg.table pruning some hi-c signal, anchoring rate is very low. I think if the hi-c signal were filtered too much? So my question is how to achieve selective retention of hi-c signal, or if I can skip this step? PS: What's the function of the first two columns of Allele.ctg.table? Becuase I find the result of haphazard second column not change a bit.

Thanks so much!