.gitignore
LICENSE
Makefile
README.md
README_old.md
VERSION
align.py
ard.py
bincon.py
classes.py
clean.py
clean3.py
color.py
color2.py
con.py
con3.py
con_to_ncc.sh
cv.py
dedup.py
dip-c
dip-c.sh
dip_c_version.py
dist.py
exp.py
force.py
impute.py
impute3.py
info.py
mgcolor.py
mkcon.py
nuc_dynamics.sh
pd.py
pos.py
pyproject.toml
pytest.ini
reg.py
reg3.py
rg.py
seg.py
tad.py
vis.py
.vscode/settings.json
code_for_tan_science_2023/multiome_archr.R
code_for_tan_science_2023/multiome_liger.R
code_for_tan_science_2023/multiome_seurat.R
color/hg19.cg.20k.hom.txt
color/hg19.cg.20k.txt
color/hg19.chr.cen
color/hg19.chr.hom.len
color/hg19.chr.len
color/hg19.chr.txt
color/hg19.cpg.100k.hom.txt
color/hg19.cpg.100k.txt
color/hg19.cpg.1m.hom.txt
color/hg19.cpg.1m.txt
color/hg19.cpg.20k.hom.txt
color/hg19.cpg.20k.rank.txt
color/hg19.cpg.20k.txt
color/hg19.cpg.500k.hom.txt
color/hg19.cpg.500k.txt
color/hg38.chr.len
color/hg38.chr.txt
color/hg38.cpg.100k.txt
color/hg38.cpg.1m.txt
color/hg38.cpg.20k.txt
color/mm10.cg.20k.txt
color/mm10.chr.cen
color/mm10.chr.hom.len
color/mm10.chr.len
color/mm10.chr.txt
color/mm10.cpg.100k.txt
color/mm10.cpg.1m.txt
color/mm10.cpg.20k.txt
images/bincon.png
images/bincon_imputed.png
images/coverage-badge.svg
images/juicebox.png
images/juicebox_imputed.png
images/logo.png
images/logo_small.png
images/pymol.cpg.png
images/pymol.exp.n.label.png
images/pymol.exp.n.png
images/pymol.n.png
legacy/ab.py
legacy/ab_dip.py
legacy/align.py
legacy/around.py
legacy/around_intra.py
legacy/around_old.py
legacy/assign.py
legacy/assign3.py
legacy/assign_old.py
legacy/assign_original.py
legacy/bincount_snp_txt.py
legacy/calc_rmsd.py
legacy/center_distance.py
legacy/chic.py
legacy/clean.py
legacy/clean_3dg.py
legacy/clean_3dg_quantile.py
legacy/clean_junk.py
legacy/clean_phase.py
legacy/cluster_gyration.py
legacy/cluster_gyration_boxes.py
legacy/cluster_gyration_lines.py
legacy/common_ab.py
legacy/common_ab_dip.py
legacy/contact.py
legacy/correct.py
legacy/count_snp_chr_txt.py
legacy/count_snp_txt.py
legacy/dclean.py
legacy/dedup.py
legacy/dedup_cluster.py
legacy/dedup_sort.py
legacy/dist.py
legacy/dist_dip_quantile.py
legacy/dist_quantile.py
legacy/distance.py
legacy/gap.py
legacy/get_hapx.py
legacy/group_chr_txt.py
legacy/group_txt.py
legacy/gyration.py
legacy/illumina.py
legacy/impute.py
legacy/impute_all.py
legacy/impute_conflict.py
legacy/impute_cross.py
legacy/impute_old.py
legacy/impute_par.py
legacy/impute_weighted.py
legacy/length.py
legacy/loop.py
legacy/mean.py
legacy/merge_ab.py
legacy/merge_phasing.py
legacy/original.py
legacy/pairwise_distance.py
legacy/pairwise_distance_corr.py
legacy/pairwise_distance_ks.py
legacy/pairwise_distance_median.py
legacy/pairwise_distance_u.py
legacy/pca.py
legacy/phase.py
legacy/phase_sperm.py
legacy/phase_txt.py
legacy/precontact.py
legacy/radius.py
legacy/sanger.py
legacy/simulate.py
legacy/snv.py
legacy/snv_sperm.py
legacy/to_cif.py
legacy/to_cif_ab.py
legacy/to_cif_ali.py
legacy/to_cif_contacts.py
legacy/to_cif_cpg.py
legacy/to_cif_hap.py
legacy/to_cif_rna.py
legacy/translate.py
legacy/translate_3dg.py
legacy/translate_clean.py
legacy/trio.py
legacy/violate.py
patch/README.md
patch/dyn_util.pyx
patch/nuc_dynamics.py
patch/pdbx_reader_escape_sequences.patch
patch/trim.c
pymol/color_centromere.py
pymol/color_centromere_legend.pdf
pymol/color_chromosomes.py
pymol/color_locus_legend.pdf
pymol/color_methylation.py
pymol/color_radial_legend.pdf
pymol/dip_c_color.py
pymol/pymol_ard.py
pymol/pymol_movie_exp.py
pymol/pymol_tad.py
release/prepare_release.sh
scripts/cen_to_leg.sh
scripts/cg.sh
scripts/color_chr_len_to_hom.sh
scripts/color_chr_to_hom.sh
scripts/color_to_rank.py
scripts/con_imputed_to_juicer_pre_short.sh
scripts/con_to_juicer_pre_short.sh
scripts/con_to_matlab_human.sh
scripts/con_to_matlab_mouse.sh
scripts/cpg.sh
scripts/hickit_3dg_to_3dg.sh
scripts/hickit_3dg_to_3dg_rescale_backbone.sh
scripts/hickit_3dg_to_3dg_rescale_unit.sh
scripts/hickit_impute_pairs_to_con.sh
scripts/hickit_impute_separated_pairs_to_con.sh
scripts/hickit_pairs_to_con.sh
scripts/name_color_x_y_z_to_cif.py
scripts/network.py
scripts/network_around.py
scripts/snp_sanger_b6_cast.py
scripts/snp_sanger_cast_129s1.py
scripts/snp_sanger_cast_b6.py
scripts/stack_row_np_int.py
scripts/sum_np_int.py
snps/NA12878.txt.gz
src/dip_c/__init__.py
src/dip_c/_version.py
src/dip_c/classes.py
src/dip_c/cli.py
src/dip_c/commands/__init__.py
src/dip_c/commands/align.py
src/dip_c/commands/ard.py
src/dip_c/commands/bincon.py
src/dip_c/commands/clean.py
src/dip_c/commands/clean3.py
src/dip_c/commands/color.py
src/dip_c/commands/color2.py
src/dip_c/commands/con.py
src/dip_c/commands/con3.py
src/dip_c/commands/cv.py
src/dip_c/commands/dedup.py
src/dip_c/commands/dist.py
src/dip_c/commands/exp.py
src/dip_c/commands/force.py
src/dip_c/commands/impute.py
src/dip_c/commands/impute3.py
src/dip_c/commands/info.py
src/dip_c/commands/mgcolor.py
src/dip_c/commands/mkcon.py
src/dip_c/commands/pd.py
src/dip_c/commands/pos.py
src/dip_c/commands/reg.py
src/dip_c/commands/reg3.py
src/dip_c/commands/rg.py
src/dip_c/commands/seg.py
src/dip_c/commands/tad.py
src/dip_c/commands/vis.py
src/dip_c/data/__init__.py
src/dip_c/data/color/hg19.cg.20k.hom.txt.gz
src/dip_c/data/color/hg19.cg.20k.txt.gz
src/dip_c/data/color/hg19.chr.cen.gz
src/dip_c/data/color/hg19.chr.hom.len.gz
src/dip_c/data/color/hg19.chr.len.gz
src/dip_c/data/color/hg19.chr.txt.gz
src/dip_c/data/color/hg19.cpg.100k.hom.txt.gz
src/dip_c/data/color/hg19.cpg.100k.txt.gz
src/dip_c/data/color/hg19.cpg.1m.hom.txt.gz
src/dip_c/data/color/hg19.cpg.1m.txt.gz
src/dip_c/data/color/hg19.cpg.20k.hom.txt.gz
src/dip_c/data/color/hg19.cpg.20k.rank.txt.gz
src/dip_c/data/color/hg19.cpg.20k.txt.gz
src/dip_c/data/color/hg19.cpg.500k.hom.txt.gz
src/dip_c/data/color/hg19.cpg.500k.txt.gz
src/dip_c/data/color/hg38.chr.len.gz
src/dip_c/data/color/hg38.chr.txt.gz
src/dip_c/data/color/hg38.cpg.100k.txt.gz
src/dip_c/data/color/hg38.cpg.1m.txt.gz
src/dip_c/data/color/hg38.cpg.20k.txt.gz
src/dip_c/data/color/mm10.cg.20k.txt.gz
src/dip_c/data/color/mm10.chr.cen.gz
src/dip_c/data/color/mm10.chr.hom.len.gz
src/dip_c/data/color/mm10.chr.len.gz
src/dip_c/data/color/mm10.chr.txt.gz
src/dip_c/data/color/mm10.cpg.100k.txt.gz
src/dip_c/data/color/mm10.cpg.1m.txt.gz
src/dip_c/data/color/mm10.cpg.20k.txt.gz
src/run_dipc.egg-info/PKG-INFO
src/run_dipc.egg-info/SOURCES.txt
src/run_dipc.egg-info/dependency_links.txt
src/run_dipc.egg-info/entry_points.txt
src/run_dipc.egg-info/requires.txt
src/run_dipc.egg-info/top_level.txt
tests/README.md
tests/__init__.py
tests/requirements.txt
tests/run_tests.sh
tests/test_classes.py