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