inverted the start and stop positions in the output gff when the stop was before the start (in inverted regions)

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

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

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

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