menu() {
    while true
    do
        printf "\n please make a selection from the MENU \n
        ==================================
        \t 1  Incidental Findings
        \t 2  CHARGE Syndrome
        \t 3  PFS Syndrome
        \t 4  Other
        ==================================\n\n"
        printf "\t Your choice: "; read menu_choice

        case "$menu_choice" in
        1) incidental ;;
        2) charge ;;
        3) pfs ;;
        4) other ;;
        *) printf "\n Invalid choice."; sleep 2 ;;
        esac
    done
}
echo "$menu_choice"

charge() {
printf "\n\n"
printf "the charge syndrome genes will now be loaded and used to calculate coverage\n"
logfile=/home/cmccabe/Desktop/NGS/API/2-12-2015/process.log
for f in /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/*base_counts.txt ; do
     echo "Start custom panel creation: $(date) - File: $f"
     bname=$(basename $f)
     pref=${bname%%.txt}
     awk '
 NR == FNR {input[$0]; next}
 {
    split($5, a, "-")
    if (a[1] in input) {
         key = $4 OFS $5
         n[key]++
         sum[key] += $7
     }
 }
 END {
     for (key in n) 
         printf "%s %.1f\n", key, sum[key]/n[key]
 }
' /home/cmccabe/Desktop/panels/CHARGE_unix.bed $f | awk '{split($2,a,"-"); print a[1] "\t" $0}' | sort | cut -f2-> /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/${pref}_Chargecoverage.bed
      echo "End custom panel creation: $(date) - File: $f"
done >> "$logfile"
printf "coverage calculated and log created\n"
}
pfs() {
printf "\n\n"
printf "the pfs syndrome genes will now be loaded and used to calculate coverage\n"
logfile=/home/cmccabe/Desktop/NGS/API/2-12-2015/process.log
for f in /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/*base_counts.txt ; do
     echo "Start custom panel creation: $(date) - File: $f"
     bname=$(basename $f)
     pref=${bname%%.txt}
     awk '
 NR == FNR {input[$0]; next}
 {
    split($5, a, "-")
    if (a[1] in input) {
         key = $4 OFS $5
         n[key]++
         sum[key] += $7
     }
 }
 END {
     for (key in n) 
         printf "%s %.1f\n", key, sum[key]/n[key]
 }
' /home/cmccabe/Desktop/panels/PFS_unix.bed $f | awk '{split($2,a,"-"); print a[1] "\t" $0}' | sort | cut -f2-> /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/${pref}_Pfscoverage.bed
      echo "End custom panel creation: $(date) - File: $f"
done >> "$logfile"
printf "coverage calculated and log created\n"
}
other() {
printf "\n\n"
printf "Please enter the gene(s) of interest, use a comma between multiple: "; IFS="," read -a gene
        printf "the indicated genes will now be loaded and used to calculate coverage\n"
        [ -z "$gene" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && return
        [ "$gene" = "end" ] && printf "\n Leaving match function." && sleep 2 && return
        for ((i=0; i<${#gene[@]}; i++))

logfile=/home/cmccabe/Desktop/NGS/API/2-12-2015/process.log
for f in /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/*base_counts.txt ; do
     echo "Start custom panel creation: $(date) - File: $f"
     bname=$(basename $f)
     pref=${bname%%.txt}
     awk '
 NR == FNR {input[$0]; next}
 {
    split($5, a, "-")
    if (a[1] in input) {
         key = $4 OFS $5
         n[key]++
         sum[key] += $7
     }
 }
 END {
     for (key in n) 
         printf "%s %.1f\n", key, sum[key]/n[key]
 }
' /home/cmccabe/Desktop/panels/$gene $f | awk '{split($2,a,"-"); print a[1] "\t" $0}' | sort | cut -f2-> /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/${pref}_genescoverage.bed
      echo "End custom panel creation: $(date) - File: $f"
done >> "$logfile"
printf "coverage calculated and log created\n"
}

while true; do
    read -p "Do you want to get coverage of a specific panel?" yn
    case $yn in
        [Yy]* ) menu; break;;
        [Nn]* ) exit;;
        * ) echo "Please answer yes or no.";;
    esac
done