Parse arguments in bash

parse_args.sh

# Parse Arguments --------------------------------------------------------------
# reference: https://stackoverflow.com/a/14203146
POSITIONAL=()
while [[ $# -gt 0 ]]; do
  key="$1"

  case $key in
      -v|--vcf)
      vcf="$2"
      shift # past argument
      shift # past value
      ;;
      -b|--bam)
      bam="$2"
      shift # past argument
      shift # past value
      ;;
      -o|--output)
      bam_noSNP="$2"
      shift # past argument
      shift # past value
      ;;
      -c|--clip)
      clip="$2"
      shift # past argument
      shift # past value
      ;;
      *)    # unknown option
      POSITIONAL+=("$1") # save it in an array for later
      shift # past argument
      ;;
  esac
done
set -- "${POSITIONAL[@]}" # restore positional parameters

echo vcf = "${vcf}"
echo bam = "${bam}"
echo output = "${bam_noSNP}"
echo clip = "${clip}"