From 881b5166dd9549c3f75b5e19363e9c60d006c193 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Thu, 28 Jul 2022 09:27:38 +0200
Subject: [PATCH 1/2] add `--version` flag

---
 pggb | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/pggb b/pggb
index a872aef..344c8d4 100755
--- a/pggb
+++ b/pggb
@@ -45,6 +45,7 @@ keep_intermediate_files=false
 compress=false
 normalize=true
 vcf_spec=false
+show_version=false
 
 if [ $# -eq 0 ]; then
     show_help=true
@@ -52,7 +53,7 @@ fi
 
 # read the options
 cmd=$0" "$@
-TEMP=`getopt -o i:o:D:a:p:n:s:l:K:F:k:x:f:B:H: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:,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: -n 'pggb' -- "$@"`
+TEMP=`getopt -o i:o:D:a:p:n:s:l:K:F:k:x:f:B:H:j:P:O:Me:t:T:vhASY:G:Q:d:I:R:NbrmZzV: --long input-fasta:,output-dir:,temp-dir:,input-paf:,map-pct-id:,n-mappings:,segment-length:,block-length-min:,mash-kmer:,mash-kmer-thres:,min-match-length:,sparse-map:,sparse-factor:,transclose-batch:,n-haps:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,poa-threads:,skip-viz,do-layout,help,no-merge-segments,do-stats,exclude-delim:,poa-length-target:,poa-params:,poa-padding:,run-abpoa,global-poa,write-maf,consensus-spec:,consensus-prefix:,pad-max-depth:,block-id-min:,block-ratio-min:,no-splits,resume,keep-temp-files,multiqc,compress,vcf-spec:,version -n 'pggb' -- "$@"`
 eval set -- "$TEMP"
 
 # extract options and their arguments into variables.
@@ -96,11 +97,21 @@ while true ; do
         -Z|--compress) compress=true ; shift ;;
         -V|--vcf-spec) vcf_spec=$2 ; shift 2 ;;
         -h|--help) show_help=true ; shift ;;
+        --version) show_version=true ; shift ;;
         --) shift ; break ;;
         *) echo "$2" "Internal error!" ; exit 1 ;;
     esac
 done
 
+if [ $show_version == true ]; then
+    SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+    cd "$SCRIPT_DIR"
+    GIT_VERSION=$(git describe --always --tags)
+    echo "pggb $GIT_VERSION"
+    cd - &> /dev/null
+    exit
+fi
+
 # if a PAF is given as input, we set the segment_length by to an arbitrary number, since we will skip the wfmash alignment process
 if [[ $input_paf != false ]]; then
     if [[ $segment_length == false ]];     then

From 58b36e353b1c1590e91cee0c7a3c2402e47d653b Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Thu, 28 Jul 2022 09:31:58 +0200
Subject: [PATCH 2/2] mention `--version` in the description

---
 pggb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pggb b/pggb
index 344c8d4..37ccf3e 100755
--- a/pggb
+++ b/pggb
@@ -250,6 +250,7 @@ if [ $show_help ]; then
     echo "    -A, --keep-temp-files       keep intermediate graphs"
     echo "    -Z, --compress              compress alignment (.paf), graph (.gfa, .og), and MSA (.maf) outputs with pigz,"
     echo "                                and variant (.vcf) outputs with bgzip"
+    echo "    --version                   display the version of pggb"
     echo "    -h, --help                  this text"
     echo
     echo "Use wfmash, seqwish, smoothxg, odgi, gfaffix, and vg to build, project and display a pangenome graph."