bash: command line arguments as script triggers - bash

Question

In my bash routine I am using two alternative methods to use arguments defined during the script execution and assign them to specific variables used by some other functions within the same script:
# tested and works OK
parse_args() {
MY_SORT_METHOD=1 # sort strings according the number of the ligand
MY_FILT_METHOD=0 # filt data according to all strategies
while (($#)); do
case "$1" in
--sort=*)
IFS== read -r _ val <<<"$1"
case "$val" in 1|2) ;; *)
echo "Wrong value is set: please select either the 1st or 2nd method of sorting"
return 1
esac
MY_SORT_METHOD="$val"
;;
--filt=*)
IFS== read -r _ val <<<"$1"
case "$val" in [0-4]) ;; *)
echo "Wrong value is chosen: please select one of four strategies of filtering (--filt=1,2,3,4). Othervise select all four strategies (--filt=0)"
return 1
esac
MY_FILT_METHOD="$val"
;;
esac
shift
done
}
# this does not work
parse_args2() {
args=$(getopt -o '' -l sort:,filt: -- "$#")
eval "set -- $args"
MY_SORT_METHOD=1
MY_FILT_METHOD=0
set -x
while (($#)); do
case "$1" in
--sort) MY_SORT_METHOD="$2"; shift; ;;
--filt) MY_FILT_METHOD="$2"; shift; ;;
--) shift; break; ;;
esac
shift;
done
}
While parse_args() is working OK, there is some bug in parse_args2(), which does not allow to execute this function in the simular fashion... What should I fix there, assuming that the both functions are called in the bash script just using using
parse_args $*
Also here is another function, which uses 4 different AWK scripts to process the same CSV file in the case if a variable defined in the argument is 0: "${MY_FILT_METHOD}" = "0":
filter_csv () {
for d in "${storage}"/*/; do
dir_name=${d%*/}
dir_name=$(basename "$dir_name")
[ "${MY_FILT_METHOD}" = "0" ] && awk -v min_lines=3 -F ", " 'a < $2 {for(idx=0; idx < i; idx++) {print arr[idx]} print $0; a=int($2); i=0; printed=NR} a > $2 && NR > 1 {arr[i]=$0; i++}END{if(printed <= min_lines) {for(idx = 0; idx <= min_lines - printed; idx++){print arr[idx]}}}' "${d}"/${dir_name}*_proc.csv > "${d}"/${dir_name}_str1.csv
[ "${MY_FILT_METHOD}" = "0" ] && awk -v cut1="$cut1" -v cut2="$cut2" -F ', ' 'NR == 1 {next} FNR==NR {if (max < $2) {max=$2; n=FNR+1} next} FNR <= 2 || (FNR == n && $2 > (cut1 * max)) || $2 > (cut2 * max)' "${d}"/${dir_name}*_proc.csv{,} > "${d}"/${dir_name}_str2.csv
[ "${MY_FILT_METHOD}" = "0" ] && awk -v cut3="$cut3" -v cut4="$cut4" -F ', ' 'NR == 1 {next} FNR==NR {if (maxP < $2) maxP=$2; if (minD=="" || minD > $3) minD=$3; next} FNR <= 2 || ($2 >= (cut3 * maxP) && $3 <= (cut4 * minD))' "${d}"/${dir_name}*_proc.csv{,} > "${d}"/${dir_name}_str3a.csv
[ "${MY_FILT_METHOD}" = "0" ] && awk -v cut3="$cut3" -v cut4="$cut4" -F ', ' 'NR == 1 {next} FNR==NR {if (maxP < $2) maxP=$2; if (minD=="" || minD > $3) minD=$3; next} FNR==2{p=$0} FNR == 1 || ($2 >= (cut3 * maxP) && $3 <= (cut4 * minD)) {++c; print} END {if (c==1) print p}' "${d}"/${dir_name}*_proc.csv{,} > "${d}"/${dir_name}_str3b.csv
done
Would it be possible rather to merge those 4 awk commands into one block activated by [ "${MY_FILT_METHOD}" = "0" ] && ?