How to remove small chromosomes from .hic files

[Gian Marco Franceschini]

Dear developers,
I aligned my Hi-C data to the full reference human genome, which includes also short contigs that represent alternative haplotypes or unresolved regions.
However, I would like to remove them from downstream analysis. How can I achieve this?

I considered: `juicer pre` (no longer supported),  `straw` (seems to accept only one chromosome at the time, which is not what I want), and 'hic-emt' (which did not work in my hands, resulting in Java errors that are absolutely obscure to me).

I just want to subset my .hic files to retain only chr1-22 contacts, and as it seems to be a reasonable task I wonder if I am missing a simpler solution.
Thank you

[Olga Dudchenko]

Create a chrom.sizes file that will only contain the chromosomes you would like to retain and pass that file when processing Hi-C data.