90 lines
2 KiB
Bash
Executable file
90 lines
2 KiB
Bash
Executable file
#!/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"
|