Merge pull request #237 from pangenome/unchop_gfaffix_output

unchop the GFAFfixed graph

pggb

@@ -556,6 +556,7 @@ if [[ $normalize == true ]]; then
     # Sort
     if [[ ! -s "$prefix_smoothed_output".final.og || $resume == false ]]; then
       ( $timer -f "$fmt" odgi build -t $threads -P -g "$prefix_smoothed".fix.gfa -o - -O \
+          | $timer -f "$fmt" odgi unchop -P -t $threads -i - -o - \
           | $timer -f "$fmt" odgi sort -P -p Ygs $odgi_temp_dir -t $threads -i - -o "$prefix_smoothed_output".final.og ) 2> >(tee -a "$log_file")
 
       resume=false # The PG-SGD sorting (`-pY`) is not deterministic, then all subsequent steps need to be rerun for consistency