From b4d198bc6dcfb3e8d1a0be021a290efae87a3674 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Sat, 16 Apr 2022 17:44:23 +0200
Subject: [PATCH 1/2] delete intermediate smoothed graphs

---
 pggb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pggb b/pggb
index 51818ee..71b9ff6 100755
--- a/pggb
+++ b/pggb
@@ -623,11 +623,13 @@ 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 ]] && [[ $write_maf == false ]];
   then
     rm -f "$prefix_smoothed".smooth.{gfa,og}
   fi
+
 fi
 
 if [[ $compress == true ]];

From 09e93e588f3ceaec91bb199f348de2d1d16adba4 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Sat, 16 Apr 2022 17:51:10 +0200
Subject: [PATCH 2/2] keep only one graph at the end. The final graph name ends
 with '.final'

---
 pggb | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/pggb b/pggb
index 71b9ff6..c4fc147 100755
--- a/pggb
+++ b/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
 
@@ -625,11 +623,10 @@ 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
-
 fi
 
 if [[ $compress == true ]];