set number of POA threads in smoothxg

for memory reasons

Dockerfile

@@ -56,7 +56,7 @@ RUN git clone --recursive https://github.com/ekg/seqwish \
 RUN git clone --recursive https://github.com/ekg/smoothxg \
     && cd smoothxg \
     && git pull \
-    && git checkout e39380d \
+    && git checkout e1d5548 \
     && git submodule update --init --recursive \
     && sed -i 's/-march=native/-march=haswell/g' deps/abPOA/CMakeLists.txt \
     && sed -i 's/-mcx16 //g' deps/WFA/CMakeLists.txt \

pggb

@@ -29,6 +29,7 @@ poa_params="1,19,39,3,81,1"
 do_viz=false
 do_layout=false
 threads=1
+poa_threads=0
 mapper=wfmash
 no_merge_segments=false
 do_stats=false
@@ -47,7 +48,7 @@ fi
 
 # read the options
 cmd=$0" "$@
-TEMP=`getopt -o i:o:p:n:s:l:K:k:B:w:j:P:Fe:t:vLhMSY:G:C:Q:d:I:R:NrmZ --long input-fasta:,output-dir:,map-pct-id:,n-mappings:,segment-length:,block-length-min:,mash-kmer:,min-match-length:,transclose-batch:,block-weight-max:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,do-viz,do-layout,help,no-merge-segments,do-stats,exclude-delim:,poa-length-target:,poa-params:,write-maf,consensus-spec:,consensus-prefix:,split-min-depth:,block-id-min:,block-ratio-min:,no-splits,resume,multiqc,pigz-compress -n 'pggb' -- "$@"`
+TEMP=`getopt -o i:o:p:n:s:l:K:k:B:w:j:P:Fe:t:T:vLhMSY:G:C:Q:d:I:R:NrmZ --long input-fasta:,output-dir:,map-pct-id:,n-mappings:,segment-length:,block-length-min:,mash-kmer:,min-match-length:,transclose-batch:,block-weight-max:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,poa-threads:,do-viz,do-layout,help,no-merge-segments,do-stats,exclude-delim:,poa-length-target:,poa-params:,write-maf,consensus-spec:,consensus-prefix:,split-min-depth:,block-id-min:,block-ratio-min:,no-splits,resume,multiqc,pigz-compress -n 'pggb' -- "$@"`
 eval set -- "$TEMP"
 
 # extract options and their arguments into variables.
@@ -77,6 +78,7 @@ while true ; do
         -C|--consensus-spec) consensus_spec=$2 ; shift 2 ;;
         -Q|--consensus-prefix) consensus_prefix=$2 ; shift 2 ;;
         -t|--threads) threads=$2 ; shift 2 ;;
+        -T|--poa-threads) poa_threads=$2 ; shift 2 ;;
         -v|--do-viz) do_viz=true ; shift ;;
         -L|--do-layout) do_layout=true ; shift ;;
         -S|--do-stats) do_stats=true ; shift ;;
@@ -101,6 +103,11 @@ then
     >&2 echo "Mandatory arguments -i, -s, -n, -p"
 fi
 
+if [[ $poa_threads == 0 ]];
+then
+    poa_threads=$threads
+fi
+
 if [[ $block_length == false ]];
 then
     block_length=$(echo $segment_length '*' 3 | bc)
@@ -159,6 +166,7 @@ then
     echo "    -r, --resume PATH           do not overwrite existing output from wfmash, seqwish, smoothxg in given directory"
     echo "                                [default: start pipeline from scratch in a new directory]"
     echo "    -t, --threads N             number of compute threads to use in parallel steps"
+    echo "    -T, --poa-threads N         number of compute threads to use during POA (set lower if you OOM during smoothing)"
     echo "    -Z, --pigz-compress         compress alignment (.paf), graph (.gfa, .og), and MSA (.maf) outputs with pigz"
     echo "    -h, --help                  this text"
     echo
@@ -251,6 +259,7 @@ smoothxg:
   split-min-depth:    $split_min_depth
   block-id-min:       $block_id_min
   block-ratio-min:    $block_ratio_min
+  poa_threads:        $poa_threads
 odgi:
   viz:                $do_viz
   layout:             $do_layout
@@ -314,6 +323,7 @@ do
         if [[ ! -s $prefix_smoothed.smooth.$i.gfa || $resume == false ]]; then
             $timer -f "$fmt" smoothxg \
                    -t $threads \
+                   -T $poa_threads \
                    -g "$input_gfa" \
                    -w $max_block_weight \
                    -K \
@@ -333,6 +343,7 @@ do
         if [[ ! -s $prefix_smoothed.smooth.gfa || $resume == false ]]; then
             $timer -f "$fmt" smoothxg \
                    -t $threads \
+                   -T $poa_threads \
                    -g "$input_gfa" \
                    -w $max_block_weight \
                    -K \