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

annulé le changement du calcul de la position de l'insertion sur le génome target, ça cassait trop de choses et selon l'interprétation c'est cohérent