added the conversion of path lines in walk format to be read by grannot. the path name must be #assembly_name#haplotype#sequence_name, for instance IRGSP#1#Chr1

adapted the code to do a transfer on several genomes, by clearing the features target genome paths between each genome

adapted the multicopies code to the output of -var. corrected the positions in the output gff for the inversions

added gene multicopies handling. new function detect_copies, and now the target_genome_path of child features and the transfer depend on the parent feature

changed how the features are transfered. now after the transfer of a gene, all its child features are transfered with it. this automatically sorts the output gff, and makes easier the handling of the cov and id filters (if a gene didnt pass, dont transfer its chids, etc)

now always use the function get_seg_occ to get the right segment occurence. so now the option -ann outputs the target genome gff with all the copies of the genes if -cov and -id are at 0

added a function to get the right segment occurence, given the segment_id,walk_name,feature_id,copy_id

modified how the feature paths in the target genomes are found; now several can be found, on several walks (chr/ctg); adapted how the features are transfered (only for the genome annotation transfer, not for the graph_gaf/gff, variations and alignment)

the dict segments_on_target_genome now stores the segment twice if it is present twice in a given walk. adapted the rest of the code to use the last occurence (like before, will change that later)