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