menu -> match -> convert? -> NO -> additional? -> NO -> menu
        ^               |          |         |
        |               +--> YES --+         +--> YES +
        |                                             |
        +---------------------------------------------+

#!/bin/bash

menu() {
    clear
    printf "\n MENU \n
    ==================================\n\n
    \t 1  Match patient\n
    \t 2  Exit\n\n
    ==================================\n\n"

    printf "\t Your choice: "; read menu_choice

    case "$menu_choice" in
        1) match ;;
        2) printf "\n Bye! \n\n"; exit ;;
        *) printf "\n Invalid choice."; sleep 2; menu ;;
    esac
}


match() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "What is the id of the patient to be matched  : "; read id
    printf "What panel: "; read panel

    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu

    cd 'C:\Users\cmccabe\Desktop\annovar'
    OMR=Output_Mutation_Report
    $( perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf )
    convert
}

convert() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "Does the file need to be converted? Y/N "; read convert_choice
    
    case "$convert_choice" in
        [yY]) $( perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput )
        additional ;;
        [nN]) additional ;;  
        *) convert ;;
    esac
}

additional() {
    printf "\n\n"
    printf "Are there additonal patients to be matched?  Y/N "; read match_choice

    case "$match_choice" in
        [yY]) id=""; panel=""; match ;;
        [nN]) id=""; panel=""; menu ;;  
        *) additional ;;
    esac
}

# actual start of this program
menu # run menu function