src/download_encode_eclip/merge_eclip.py: modification of merge_files function to filter onily the peaks with a score of 1000 and inside a gene (first and last exons not included)"

src/download_encode_eclip/create_gene_bed.py: script to create a bed file of human geneswithout the first and the last exons

src/find_interaction_cluster/clip_figures/clip_analyser_fake_community.py: script to create fake community based on the peak density of each genes

src/find_interaction_cluster/clip_figures/communities_similarities.py: Create the adjusted rand index heatmap of the differnts communities

src/find_interaction_cluster/clip_figures/clip_compo_analyser.py: the differents violins (enriched, imoverished) are now order in the figure with custom colors

src/find_interaction_cluster/clip_figures/clip_compo_analyser.py: chnages and creation of new functions

creation of function to handle clip results folder produced by clip_launcher_4_many_communities and modification of get_middle_group, get_extreme_groups and get_interest_groups to simplify the names of each groups + pep8 chnages

src/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: chnage tiles in merge_figures function + pep8 changes

src/download_encode_eclip/merge_eclip.py: modification of merge_files function to remove the heading chr in the first bed column

src/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: Add a step that merges the TADs before the liftover

src/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: change in liftover and check_n_save_bed function

src/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: add pointsize argument in mantage command

src/find_interaction_cluster/tad_to_communities/tad_to_communities.py: creation of functions targeted_tad_to_communities removing_chr and targeted_bedtools_intersect to convert custom TAD to communities

src/find_interaction_cluster/config.py: fix merge problem by re-creating function get_communities_basefile

src/hic_TAD_caller/create_TAD_HiC_files/__main__.py: creation of a function launcher with a parameter resolution

src/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: create for each clip the community figures obtained using many community files

src/find_interaction_cluster/clip_figures/config.py: add variables communities and communitites name

 src/hic_TAD_caller/: Script to call TADs with ArrowHead from different Hic files recovered from data.4dnucleome.org

src/nt_composition/config.py src/nt_composition/distance.py src/nt_composition/make_nt_correlation.py: change the calls of get_good_project

src/figures_utils/config_figures.py: add a parameter to get_good_project to select the cell of interest in our projects

src/download_encode_eclip/get_encode_clips.py: modifications to be hable to download  RIP-seq, iCLIP and RIP-chip experiments

src/find_interaction_cluster/__main__.py src/find_interaction_cluster/community_finder.py: add the parameter use weight

src/find_interaction_cluster/community_calibration.py: creation of input and output for hipMCL inside it's result folder