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

the prediction can now give the effect of a frameshift mutation until the next variation, even if it is on another cds part

corrected the coordinates in the graph gff and gaf. modified the positions of the segments to have them 1-based like the features

tried to adapt the code to use several cds. detected a problem in the coordinate system to correct in main

changed the reading of the variation file and the handling of its information so that it accepts cds in multiple parts