#!/bin/sh
#Lab 5: Options -g -d
echo "----start of 5c----"
MASTER="MasterFile"
GENMASTER="no"
DELMASTER="no"
#5c-Generate the Master file, if it does not exist.
DIR="10.SeS_Unit2_AdvancedControl_DataFiles/sample"
cd "$DIR"
echo "1"
echo "2"

# Process the arguments
echo "3"
echo "$@"
echo "3a"

for i in $@
do
   echo "4"
   echo "$i"
   case "$i" in
   -g) if [  -e "$MASTER"  ]
        then
          echo "MASTER file exists; please delete it"
          echo "exit 0"
          exit 0
     	fi
        echo "fi"
        GENMASTER="yes"  ;;
   *) echo "$i" is not a valid option" 1>&2
        exit 1  
   esac
   echo "6"
done
echo "7"


exit



# Handle -g case
if [ "$GENMASTER" != "no" ]
then
  ./create
  exit 0
else
  
    if [ ! -e "$MASTER" ]
    then
         echo "MASTER file does not exist; please generate it"
         #If Master File doesn't exits, exit status code 0.
         echo "exit 0"
    fi
    ./bamscan3f.sh
fi 

echo "----end of 5c----"

echo "----start of Lab 4----"
#Combine scripts 2a,3a,3b,2c,3c,3d,3e,2e
TMP=/tmp/$$
./bamscan2a.sh
./bamscan3a.sh
./bamscan3b.sh
./bamscan2c.sh
./bamscan3c.sh
echo "Changed files:"
./bamscan3d.sh  | grep '^\(<\|>\)'  | awk '{ print $NF }' | sort | uniq
./bamscan3e.sh
./bamscan2e.sh
echo "Everything ran correctly"

exit