corrected the detection of last segment for child features

Functions_output.py

@@ -40,18 +40,20 @@ def generate_target_gff(feature_id,seg_size,args,reason_features_not_transfered,
                     if seg in feature_target_path: # parent path
                         child_first_seg=seg
                         break
+
                 if child_first_seg!='': # the child may be absent in this occurence !
-                    for seg in child.segments_list_source:
-                        if seg in reversed(feature_target_path): # parent path
+                    for seg in reversed(child.segments_list_source):
+                        if seg in feature_target_path: # parent path
                             child_last_seg=seg
                             break
-
                     if inversion: # done twice, make a function
                         child_size_on_new_genome=get_feature_start_on_target_genome_inv(child_last_seg,child_id,walk,copy_id)-get_feature_stop_on_target_genome_inv(child_first_seg,child_id,walk,copy_id)+1
                     else:
                         child_size_on_new_genome=get_feature_stop_on_target_genome(child_last_seg,child_id,walk,copy_id)-get_feature_start_on_target_genome(child_first_seg,child_id,walk,copy_id)+1
                     child_size_diff=abs(child_size_on_new_genome-child.size)
 
+                    [cov,id]=get_id_cov(child_id,seg_size,feature_target_path) # change the target_path to get the childs one..... not straightforward.
+
                     # transfer the child feature:
                     line_gff=create_line_target_gff(child_first_seg,child_last_seg,child_id,child_size_diff,inversion,walk,cov,id,copy_id)
                     write_line(line_gff,output_target_gff,False)