Merge pull request #185 from pangenome/one_graph

output only one `final` graph

pggb

@@ -452,18 +452,16 @@ do
     fi
 done
 
+prefix_final_graph="$prefix_smoothed".smooth.final
 if [[ $normalize == true ]];
 then
-    prefix_final_graph="$prefix_smoothed".smooth.fix
-
     # Remove redundancy and sort
     ( $timer -f "$fmt" gfaffix "$prefix_smoothed".smooth.gfa -o "$prefix_final_graph".gfa | $timer -f "$fmt" pigz >"$prefix_final_graph".affixes.tsv.gz ) 2> >(tee -a "$log_file")
     ( $timer -f "$fmt" odgi build -t $threads -P -g "$prefix_final_graph".gfa -o - -O \
         | $timer -f "$fmt" odgi sort -P -p Ygs -t $threads -i - -o "$prefix_final_graph".og ) 2> >(tee -a "$log_file")
     ( $timer -f "$fmt" odgi view -i "$prefix_final_graph".og -g >"$prefix_final_graph".gfa ) 2> >(tee -a "$log_file")
 else
-    prefix_final_graph="$prefix_smoothed".smooth
-
+    mv "$prefix_smoothed".smooth.gfa "$prefix_final_graph".gfa
     $timer -f "$fmt" odgi build -t $threads -P -g "$prefix_final_graph".gfa -o "$prefix_final_graph".og 2> >(tee -a "$log_file")
 fi
 
@@ -623,8 +621,9 @@ fi
 if [[ $keep_intermediate_files != true ]];
 then
   rm -f "$prefix_seqwish".seqwish.{gfa,og}
+  rm -f "$prefix_smoothed".smooth.[0-9]*.{gfa,og}
 
-  if [[ $normalize == true ]] && [[ $write_maf == false ]];
+  if [[ $normalize == true ]];
   then
     rm -f "$prefix_smoothed".smooth.{gfa,og}
   fi