modified the setting of the parameter max_diff

Functions_output.py

@@ -51,7 +51,7 @@ def gff_one(first_seg,last_seg,feature_id,list_seg,max_diff):
 
 
 # writes the gff of azucena using the gff of the graph
-def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var,target_genome_name):
+def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var,target_genome_name,max_diff):
     print("generation of the genome's gff ")
 
     # create variables and open files
@@ -94,7 +94,6 @@ def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var,target_genome_na
 
         # outputs the feature once in a gff, from the first to the last segment present on the new genome
         if once:
-            max_diff=2 # maximum difference size (n times bigger of smaller)
             transfer_stat=gff_one(first_seg,last_seg,feat,list_seg,max_diff) # insertion not considered !!!
             if transfer_stat=="bad_size":
                 bad_size_features+=1

main.py

@@ -42,7 +42,8 @@ if run=="command_line":
     graph_gaf(out_gaf,gfa)
 
     # outputs the gff of a genome for the chr10
-    genome_gff(pos_seg,out_gff,gfa,out_once,out_detail,out_var,target_genome_name)
+    max_diff=2 # maximum size difference (n times bigger or smaller) between the gene on the reference genome and the gene on the target genome for the gene to be transfered.
+    genome_gff(pos_seg,out_gff,gfa,out_once,out_detail,out_var,target_genome_name,max_diff)