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 ]];