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

corrected the selection of target genomes when none are specified so that it doesnt take the source genome

adapted the code to use the arguments given by argparse, and to handle several chromosome files and several target genomes

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

commencé à réorganiser le code plus proprement.changé l'output du détail des variations, corrigé quelques erreurs de calculs de coordonnées