├── .gitignore ├── README.md ├── README_old.md ├── align.py ├── ard.py ├── bincon.py ├── classes.py ├── clean.py ├── clean3.py ├── code_for_tan_science_2023 ├── multiome_archr.R ├── multiome_liger.R └── multiome_seurat.R ├── color.py ├── color ├── hg19.cg.20k.hom.txt ├── hg19.cg.20k.txt ├── hg19.chr.cen ├── hg19.chr.hom.len ├── hg19.chr.len ├── hg19.chr.txt ├── hg19.cpg.100k.hom.txt ├── hg19.cpg.100k.txt ├── hg19.cpg.1m.hom.txt ├── hg19.cpg.1m.txt ├── hg19.cpg.20k.hom.txt ├── hg19.cpg.20k.rank.txt ├── hg19.cpg.20k.txt ├── hg19.cpg.500k.hom.txt ├── hg19.cpg.500k.txt ├── hg38.chr.len ├── hg38.chr.txt ├── hg38.cpg.100k.txt ├── hg38.cpg.1m.txt ├── hg38.cpg.20k.txt ├── mm10.cg.20k.txt ├── mm10.chr.cen ├── mm10.chr.hom.len ├── mm10.chr.len ├── mm10.chr.txt ├── mm10.cpg.100k.txt ├── mm10.cpg.1m.txt └── mm10.cpg.20k.txt ├── color2.py ├── con.py ├── con3.py ├── con_to_ncc.sh ├── cv.py ├── dedup.py ├── dip-c ├── dip-c.sh ├── dist.py ├── exp.py ├── force.py ├── images ├── bincon.png ├── bincon_imputed.png ├── juicebox.png ├── juicebox_imputed.png ├── logo.png ├── logo_small.png ├── pymol.cpg.png ├── pymol.exp.n.label.png ├── pymol.exp.n.png └── pymol.n.png ├── impute.py ├── impute3.py ├── info.py ├── legacy ├── ab.py ├── ab_dip.py ├── align.py ├── around.py ├── around_intra.py ├── around_old.py ├── assign.py ├── assign3.py ├── assign_old.py ├── assign_original.py ├── bincount_snp_txt.py ├── calc_rmsd.py ├── center_distance.py ├── chic.py ├── clean.py ├── clean_3dg.py ├── clean_3dg_quantile.py ├── clean_junk.py ├── clean_phase.py ├── cluster_gyration.py ├── cluster_gyration_boxes.py ├── cluster_gyration_lines.py ├── common_ab.py ├── common_ab_dip.py ├── contact.py ├── correct.py ├── count_snp_chr_txt.py ├── count_snp_txt.py ├── dclean.py ├── dedup.py ├── dedup_cluster.py ├── dedup_sort.py ├── dist.py ├── dist_dip_quantile.py ├── dist_quantile.py ├── distance.py ├── gap.py ├── get_hapx.py ├── group_chr_txt.py ├── group_txt.py ├── gyration.py ├── illumina.py ├── impute.py ├── impute_all.py ├── impute_conflict.py ├── impute_cross.py ├── impute_old.py ├── impute_par.py ├── impute_weighted.py ├── length.py ├── loop.py ├── mean.py ├── merge_ab.py ├── merge_phasing.py ├── original.py ├── pairwise_distance.py ├── pairwise_distance_corr.py ├── pairwise_distance_ks.py ├── pairwise_distance_median.py ├── pairwise_distance_u.py ├── pca.py ├── phase.py ├── phase_sperm.py ├── phase_txt.py ├── precontact.py ├── radius.py ├── sanger.py ├── simulate.py ├── snv.py ├── snv_sperm.py ├── to_cif.py ├── to_cif_ab.py ├── to_cif_ali.py ├── to_cif_contacts.py ├── to_cif_cpg.py ├── to_cif_hap.py ├── to_cif_rna.py ├── translate.py ├── translate_3dg.py ├── translate_clean.py ├── trio.py └── violate.py ├── mgcolor.py ├── mkcon.py ├── nuc_dynamics.sh ├── patch ├── dyn_util.pyx ├── nuc_dynamics.py └── trim.c ├── pd.py ├── pos.py ├── pymol ├── pymol_ard.py ├── pymol_movie_exp.py └── pymol_tad.py ├── reg.py ├── reg3.py ├── rg.py ├── scripts ├── cen_to_leg.sh ├── cg.sh ├── 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