prep function deprecated in the latest HiCRep version

[eternalding]

Greetings.

According to HiCRep's github (https://github.com/TaoYang-dev/hicrep/blob/master/NEWS), "prep" function is now deprecated. Is it possible to update HiCRep wrapper correspondingly?

Best regards, Wenny

[liuxiawei]

I got the sam question. This may be caused by omit step of "prep". Change into the old code so that can run well. Omit the line 93,94 of /3DChromatin_ReplicateQC/wrappers/HiCRep/HiCRep_wrapper.R add new line after that ."SCC.out = get.scc(m1_big[,-c(1:3)], m2_big[,-c(1:3)], resol, h, 0, maxdist)" I am not sure the code run rightly, but it run. After test, I think it work well,due to the code used in old commit.

[liuxiawei]

You also can download from https://genome.cshlp.org/content/early/2017/08/30/gr.220640.117.full.pdf+html to download the Supplemental_hicrep_1.0.1.tar.gz(https://genome.cshlp.org/content/suppl/2017/10/06/gr.220640.117.DC1/Supplemental_hicrep_1.0.1.tar.gz)