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

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

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

the functions that read the gfa file now read a file with only the segments or only the walk (generated with getSegmentsCoordinates), to handle smaller files

manages the arguments for the main, and handles the preprocessing of the input files (getSegmentsCoordinates and bedtools intersect)

adapted the code to handle paths without the assembly name, and to output in batch to reduce the number of file access

adapted the code to select the genomes to handle, and treat assemblies with contigs instead of chromosomes

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