added a function to order the dictionnary that stores the features. now the parent features are before their childs; it makes future manipulation of this dictionnary easier

modified the condition for the transfer. now the filters coverage and id only apply to genes. if the gene passes the filters, all its child features are transfered. if the gene doesnt pass the filters, none of its child features are transfered

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

changed the usage of id and cov; -ann is now required, and these options only work on -ann and -pav (the rest will come later)

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

added a dict that stores the size of the segments, to get the coverage and sequence id of the transfers

changed the creation of Feature objects to handle intersect files where a feature can appear after its childs, to handle complete gff files

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 keep the orientation of the segments from the walks. added functions to handle oriented segments