src/commands.sh: change gc content figure -e parameter to 2000 + coverage figure for 5y only on expressed genes

src/bed_handler/filter_bed.py: add an option keep to recover every other genes not in the filter_file

src/bed_handler/get_other_exon_in_same_gene.py: modication of outpout file name in get_other_exon_in_same_gene

src/bed_handler/select_regulated_near_ctcf_exons.py: creation of bed file with duplicate genes in create_bed_ctcf_exon

src/bed_handler/get_other_exon_in_same_gene.py: From a list of exons get the list of other exons in same gene far from a CTCF site

src/visu/figure_maker.py: removing the creation of a tmp file to speed up the creation of a figure made on the same input files

src/visu/__main__.py src/visu/figure_maker.py: modification to create a figure with two different list of exons

src/bed_handler/__main__.py: add a parameter include0 to include exons containing CTCF if wanted. Add a parameter near_ctcf that allows to recover regulated exons far from a CTCF site

src/bed_handler/select_regulated_near_ctcf_exons.py: add a parameter include0 to include exons containing CTCF if wanted. Add a parameter near_ctcf that allows to recover regulated exons far from a CTCF site

src/bed_handler/select_regulated_near_ctcf_exons.py: exon containing CTCF sites are dropped when the threshold is above 0

 src/visu/figure_maker.py src/visu/__main__.py: bin0_norm -> norm parameter that can either be a file or a bin number or None

src/bed_handler/select_regulated_near_ctcf_exons.py: modification of create_bed_ctcf_exon function to also create a bed file for genes