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