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

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)

modified the condition for the transfer. now the filters coverage and id only apply to genes. if the gene passes the filters, all its child features are transfered. if the gene doesnt pass the filters, none of its child features are transfered

the function that generates the target genomes gff now doesnt transfer if the coverage or id is too low

corrected the emptying of the dict segments_on_target_genome; this reduced the number of fragmented genes, that were due to segments from previous genome staying in the dict

adapted to keep the orientation of the segments from the walks. added functions to better handle inversions

adapted the code to use the options for the output files. changed every instance of 'clustal' to 'aln' in the code

changed when the output was writen in the output files, and changed the input of a function to adapt to changes in Functions.py

adapted the code to transfer with several chromosome files, changed where the dictionaries are made (now in main)

changed the order in which the output files are generated, to prepare for changes to reduce memory usage

replaced binary search by search in dictionary for getting the index of the segments in the target genome path