parse_args_getopt.sh

#!/usr/bin/env bash
# Time-stamp: <2017-04-27 09:57:21 kmodi>
#
# Example of using getopt to parse command line options
# http://stackoverflow.com/a/29754866/1219634 Limitation: All the options
# starting with - have to be listed in --options/--longoptions, else getopt will
# error out. So this cannot be used in wrapper scripts for other applications
# where you plan to pass on the non-wrapper-script options to that wrapped
# application.

# Initialize variables
help=0
debug=0
verbose=0
dummy_arg="__dummy__"
extra_args=("${dummy_arg}") # Because set -u does not allow undefined variables to be used
discard_opts_after_doubledash=0 # 1=Discard, 0=Save opts after -- to ${extra_args}

echo "All pre-getopt arguments: $*"

getopt --test > /dev/null
if [[ $? -ne 4 ]]; then
    echo "I'm sorry, 'getopt --test' failed in this environment."
    exit 1
fi

# An option followed by a single colon ':' means that it *needs* an argument.
# An option followed by double colons '::' means that its argument is optional.
# See `man getopt'.
SHORT=hDvo:                     # List all the short options
LONG=help,debug,verbose,output: # List all the long options

# - Temporarily store output to be able to check for errors.
# - Activate advanced mode getopt quoting e.g. via "--options".
# - Pass arguments only via   -- "$@"   to separate them correctly.
# - getopt auto-adds "--" at the end of ${PARSED}, which is then later set to
#   "$@" using the set command.
PARSED=$(getopt --options ${SHORT} \
                --longoptions ${LONG} \
                --name "$0" \
                -- "$@")         #Pass all the args to this script to getopt
if [[ $? -ne 0 ]]; then
    # e.g. $? == 1
    #  then getopt has complained about wrong arguments to stdout
    exit 2
fi
# Use eval with "$PARSED" to properly handle the quoting
# The set command sets the list of arguments equal to ${PARSED}.
eval set -- "${PARSED}"

echo "Getopt parsed arguments: ${PARSED}"
echo "Effective arguments: $*"
echo "Num args: $#"

while [[ ( ${discard_opts_after_doubledash} -eq 1 ) || ( $# -gt 0 ) ]]
do
    echo "parsing arg: $1"
    case "$1" in
        -o|--output) shift
                     out_file="$1";;
        -h|--help) help=1;;
        -D|--debug) debug=1;;
        -v|--verbose) verbose=1;;
        --) if [[ ${discard_opts_after_doubledash} -eq 1 ]]; then break; fi;;
        *) extra_args=("${extra_args[@]}" "$1");;
    esac
    shift                       # Expose the next argument
done

# Now delete the ${dummy_arg} from ${extra_args[@]} array # http://stackoverflow.com/a/16861932/1219634
extra_args=("${extra_args[@]/${dummy_arg}}")

echo "help: ${help}, debug: ${debug}, verbose: ${verbose}, in: $1, out: $out_file, extra args=${extra_args[*]}"

This puts all positional arguments, even those before the -- into extra args. The intention of in: $1 on the final line is unclear to me as $1 is always undefined by this point.

I've made an update to address these concerns, as well as some minor cleanup (like using declare for lists rather than dummy_arg).