From 250dc2d0bf88d9726696679acfe3d6d90661cdc0 Mon Sep 17 00:00:00 2001
From: Rodolphe Breard <rodolphe@what.tf>
Date: Sat, 5 Sep 2015 16:03:34 +0200
Subject: [PATCH] arguments parsing

---
 vcf_compressor.sh | 90 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)
 create mode 100755 vcf_compressor.sh

diff --git a/vcf_compressor.sh b/vcf_compressor.sh
new file mode 100755
index 0000000..3ddc164
--- /dev/null
+++ b/vcf_compressor.sh
@@ -0,0 +1,90 @@
+#!/bin/bash
+## Copyright (c) 2015 Rodolphe Breard
+## 
+## This program is free software: you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 3 of the License, or
+## (at your option) any later version.
+## 
+## This program is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+## 
+## You should have received a copy of the GNU General Public License
+## along with this program.  If not, see <http://www.gnu.org/licenses/>.
+##
+
+set -euo pipefail
+IFS=$'\n\t'
+
+version () {
+    echo "VCF Compressor 0.1.0-dev"
+    exit 0
+}
+
+usage () {
+    exit_status="${1:-1}"
+    echo "Usage: vcf_compressor [OPTION]... VCF_FILE"
+    echo ""
+    echo "Options:"
+    echo "  -o, --output"
+    echo "  -v, --verbose"
+    echo "  -V, --version"
+    echo "  -h, --help"
+    exit "$exit_status"
+}
+
+echo_verbose () {
+    if [ $verbose -gt 0 ]; then
+        echo "$@"
+    fi
+}
+
+input_file=""
+output_file=""
+verbose=0
+
+while :; do
+    test $# -gt 0 || break
+    case "$1" in
+        -o|--output)
+            if [ -n "$2" ]; then
+                output_file="$2"
+                shift 2
+                continue
+            else
+                usage
+            fi
+            ;;
+        -v|--verbose)
+            verbose=1
+            shift
+            ;;
+        -V|--version)
+            version
+            ;;
+        -h|--help)
+            usage 0
+            ;;
+        *)
+            if [ -z "$input_file" ]; then
+                input_file="$1"
+                shift
+                continue
+            else
+                usage
+            fi
+            ;;
+    esac
+done
+test -z "$input_file" && usage
+if [ -z "$output_file" ]; then
+    dir=$(dirname "$input_file")
+    name=$(basename "$input_file" ".vcf")
+    output_file="$dir/$name.new.vcf"
+fi
+
+echo "in:  $input_file"
+echo "out: $output_file"
+echo_verbose "verbose mode on"