Merge pull request #317 from mbhall88/patch-1

make stats option consistent with help

pggb

@@ -117,7 +117,7 @@ fi
 
 # read the options
 cmd=$0" "$@
-TEMP=`getopt -o i:o:D:a:p:n:s:l:K:F:k:x:f:B:XH:j:P:O:Me:t:T:vhASY:G:Q:d:I:R:NbrmZzV: --long input-fasta:,output-dir:,temp-dir:,input-paf:,map-pct-id:,n-mappings:,segment-length:,block-length-min:,mash-kmer:,mash-kmer-thres:,min-match-length:,sparse-map:,sparse-factor:,transclose-batch:,skip-normalization,n-haps:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,poa-threads:,skip-viz,do-layout,help,no-merge-segments,do-stats,exclude-delim:,poa-length-target:,poa-params:,poa-padding:,run-abpoa,global-poa,write-maf,consensus-spec:,consensus-prefix:,pad-max-depth:,block-id-min:,block-ratio-min:,no-splits,resume,keep-temp-files,multiqc,compress,vcf-spec:,version -n 'pggb' -- "$@"`
+TEMP=`getopt -o i:o:D:a:p:n:s:l:K:F:k:x:f:B:XH:j:P:O:Me:t:T:vhASY:G:Q:d:I:R:NbrmZzV: --long input-fasta:,output-dir:,temp-dir:,input-paf:,map-pct-id:,n-mappings:,segment-length:,block-length-min:,mash-kmer:,mash-kmer-thres:,min-match-length:,sparse-map:,sparse-factor:,transclose-batch:,skip-normalization,n-haps:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,poa-threads:,skip-viz,do-layout,help,no-merge-segments,stats,exclude-delim:,poa-length-target:,poa-params:,poa-padding:,run-abpoa,global-poa,write-maf,consensus-spec:,consensus-prefix:,pad-max-depth:,block-id-min:,block-ratio-min:,no-splits,resume,keep-temp-files,multiqc,compress,vcf-spec:,version -n 'pggb' -- "$@"`
 eval set -- "$TEMP"
 
 # extract options and their arguments into variables.
@@ -150,7 +150,7 @@ while true ; do
         #-C|--consensus-spec) consensus_spec=$2 ; shift 2 ;;
         -Q|--consensus-prefix) consensus_prefix=$2 ; shift 2 ;;
         -v|--skip-viz) do_viz=false ; do_layout=false; shift ;;
-        -S|--do-stats) do_stats=true ; shift ;;
+        -S|--stats) do_stats=true ; shift ;;
         -V|--vcf-spec) vcf_spec=$2 ; shift 2 ;;
         -m|--multiqc) multiqc=true ; shift ;;
         -o|--output-dir) output_dir=$2 ; shift 2 ;;