awk -F'|' 'NR==FNR && NR>1 {a[++i]=$1$3;next}   #Read first file i.e. control_file starting from line 2 and fill the  array 'a' with value $1$3 i.e. Key and output field
            FNR>1 { if (b[FNR]) { c[FNR]=$0} else { b[FNR]=$0} } #Read file1 and file2 and fill the array 'b' for file1 and 'c' for file2
            END {
                for(k in c) {
                             split(c[k],d,"|");split(b[k],e,"|") ; # fill the array 'd' and 'e' by spilting record into fields of file1 and file2
                             for (j=1;j<=6;j++) {
                                                 if (a[j]=="YY") { #if key and output both are 'Y' then print the field as it is
                                                                  printf "%s|", d[j]
                                                                  } 
                                                 else if(a[j] != "NN") {  #if key and output both are not 'N'
                                                                        printf "%s|" ,(d[j]==e[j])?"Y":"N" #if field from file1 and file2 same then print 'Y' else 'N'
                                                                        }
                                                  }printf "\n"
                             }
                 }' control_file file1 file2