#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>

void shift(char* string);
int getlines(FILE* stream, char** line, ssize_t* nread, int* ntot, size_t len);
char* normalize(char* string, int nflag);
void clean(char* string);
void divideString(char* string, int n);
void debacon(char* string, int btype);
void flip(char* string);
void deHex(char* string);
void deRNA(char* string);
int verbose = 0;


int main(int argc, char* argv[]){
FILE* scram;
int opt;
int fcheck = 0;
int nflag = 0;
int btype = 0;
int bitflip = 0;
char** line = malloc(sizeof(char *) * 16);
int i = 0;
int j = 0;
int k = 0;
size_t len = 0;
ssize_t nread[16];
int ntot = 0;
char buffer[1024];
char temp[1024];
int runBacon = 0;
int runHex = 0;
int runDNA = 0;

while((opt = getopt(argc, argv, "hvf:a:n:i:HBD")) != -1){
switch(opt){
case 'h':
printf("\nUSAGE: ./decode -f path_to_input_file type_of_decode options\n");
printf("OPTIONS: -f [FILENAME] to specify input file\n");
printf("OPTIONS: -v for verbose mode\n");
printf("OPTIONS: -a [a or b] to specify which type of bacon alphebet (Bacon Cypher Only)\n");
printf("OPTIONS: -n [0 or 1 or 2 or 3] to specify how the bitstring should be read\n");
printf("OPTIONS: -i [t or f] to specify how 0's and 1's are read from the bitstring\n");
printf("OPTIONS: -B for Bacon Cypher\n");
printf("OPTIONS: -H for HEX conversion\n");
printf("OPTIONS: -D for DNA RNA Stop Codon Cypher\n");
printf("OPTIONS: -h displays this menu\n");
printf("\nEXAMPLE: ./decode -f file -B -a b -n 2 -i f -v\n");
exit(EXIT_SUCCESS);
case 'f':
scram = fopen(optarg, "r");
fcheck = 1;
break;
case 'v':
printf("\nTurning on Verbose Mode...\n");
verbose = 1;
break;
case 'a':
if(optarg[0] == 'a' || optarg[0] == 'A'){
btype = 0;
} else if(optarg[0] == 'b' || optarg[0] == 'B'){
btype = 1;
} else{
printf("\nERROR: Invalid argument for for -a option, must be a or b\n");
exit(EXIT_FAILURE);
}
break;
case 'n':
if(atoi(optarg) < 4){
nflag = atoi(optarg);
} else{
printf("\nERROR: Invalid argument for -n option, must be 0, 1, 2, or 3\n");
}
break;
case 'i':
if(optarg[0] == 't' || optarg[0] == 'T'){
bitflip = 1;
}
break;
case 'B':
if(runHex == 1){
printf("\nERROR: Cannot run Bacon Cypher and Hex conversion together\n");
exit(EXIT_FAILURE);
} else if(runDNA == 1){
printf("\nERROR: Cannot run Bacon Cypher and DNA RNA conversion together\n");
exit(EXIT_FAILURE);
} else{
runBacon = 1;
}
break;
case 'H':
if(runBacon == 1){
printf("\nERROR: Cannot run Bacon Cypher and Hex conversion together\n");
exit(EXIT_FAILURE);
} else if(runDNA== 1){
printf("\nERROR: Cannot run DNA RNA Cypher and Hex conversion together\n");
exit(EXIT_FAILURE);
} else{
runHex = 1;
}
break;
case 'D':
if(runHex == 1){
printf("\nERROR: Cannot run Hex conversion and DNA RNA Cypher together\n");
exit(EXIT_FAILURE);
} else if(runBacon == 1){
printf("\nERROR: Cannot run Bacon Cypher and DNA RNA Cypher together\n");
exit(EXIT_FAILURE);
} else{
runDNA = 1;
}
break;
default:
printf("ERROR: Unrecognized option, try -h\n");
exit(EXIT_FAILURE);
}
}

if(fcheck == 0){
printf("ERROR: Must specify input file, try -h\n");
exit(EXIT_FAILURE);
} else if(argc <=3){
printf("ERROR: Must specify -H, -B, or -D.., try -h for help\n");
}

i = getlines(scram, line, nread, &ntot, len);

if(verbose == 1){
for(j = 0; j < i; j++){
printf("Retrieved line of length %zu:\n", nread[j]);
printf("line %i is: %s\n", j, line[j]);
}
printf("Total Characters Read: %i\n\n", ntot);
j = 0;
}

if(runDNA == 1){
for(j = 0; j < i; j++){
line[j] = normalize(line[j], 8);
}
j = 1;
strcpy(buffer, line[0]);
for(j = 1; j < i; j++){
strcat(buffer, line[j]);
}

if(verbose == 1){
printf("\nCombined String: %s\n", buffer);
}

for(k = 0; k <= strlen(buffer); k++){
divideString(buffer, 3);
if(verbose == 1){
printf("\nString split into 3's for decoding:\n");
printf("%s\n", buffer);
printf("\nDNA RNA Cypher Decode\n");
}
deRNA(buffer);
shift(buffer);
}
for(j = 0; j <= i; j++){
free(line[j]);
}
fclose(scram);
return 0;
}

for(j = 0; j < i; j++){
        if(verbose == 1){
                printf("Normalizeing line %i\n", j);
                }
                if(bitflip == 1){
                flip(line[j]);
                }
                line[j] = normalize(line[j], nflag);
                if(verbose == 1){
                printf("Line %i is now: %s\n", j, line[j]);
                }
}
       
        j = 1;
        strcpy(buffer, line[0]);
        for(j = 1; j < i; j++){
        strcat(buffer, line[j]);
        }
       
        if(verbose == 1){
        printf("\nCombined String: %s\n", buffer);
        }


if(runBacon == 1){
for(k = 0; k <= strlen(buffer); k++){
divideString(buffer, 5);
if(verbose == 1){
printf("\nString split into 5's for decoding:\n");
printf("%s\n", buffer);

printf("\nDebaconing:\n");
}
debacon(buffer, btype);

shift(buffer);
}
}

if(runHex == 1){
for(k = 0; k <= strlen(buffer); k++){
if(strlen(buffer)%4 != 0){
switch(strlen(buffer)%4){
case 1:
temp[0] = '0';
temp[1] = '0';
temp[2] = '0';
temp[3] = '\0';
strcat(temp, buffer);
break;
case 2:
temp[0] = '0';
temp[1] = '0';
temp[2] = '\0';
strcat(temp, buffer);
break;
case 3:
temp[0] = '0';
temp[1] = '\0';
strcat(temp, buffer);
break;
default:
printf("Something bad happened...\n");
break;
}
} else{
strcpy(temp, buffer);
}
divideString(temp, 4);
if(verbose == 1){
printf("\nString split into 4's\n");
printf("%s\n", temp);
printf("\nConverting to Hex:\n");
}
deHex(temp);
clean(temp);
shift(buffer);

}
}
j = 0;
for(j = 0; j <= i; j++){
free(line[j]);
}
free(line);
fclose(scram);
return 0;
}

void flip(char *string){
char *i;
for(i=string; *i; i++){
if(*i == '1'){
*i = '0';
} else if(*i == '0'){
*i = '1';
}
}
}

void deRNA(char *string){
char buffer[4];
int i = 0;

while(string[i] != '\0'){
buffer[0] = string[i];
i++;
buffer[1] = string[i];
i++;
buffer[2] = string[i];
buffer[3] = '\0';
i+=2;

if(strcmp(buffer, "yyy") == 0 || strcmp(buffer, "YYY") == 0 || strcmp(buffer, "ttt") == 0 || strcmp(buffer, "TTT") == 0 || strcmp(buffer, "uuu") == 0 || strcmp(buffer, "UUU") == 0){
printf("F");
} if(strcmp(buffer, "yyp") == 0 || strcmp(buffer, "YYP") == 0 || strcmp(buffer, "yyb") == 0 || strcmp(buffer, "YYB") == 0){
printf("F");
} if(strcmp(buffer, "yyo") == 0 || strcmp(buffer, "YYO") == 0){
printf("L");
} if(strcmp(buffer, "yyg") == 0 || strcmp(buffer, "YYG") == 0){
printf("L");
} if(strcmp(buffer, "pyy") == 0 || strcmp(buffer, "PYY") == 0 || strcmp(buffer, "byy") == 0 || strcmp(buffer, "BYY") == 0){
printf("L");
} if(strcmp(buffer, "pyp") == 0 || strcmp(buffer, "PYP") == 0 || strcmp(buffer, "byb") == 0 || strcmp(buffer, "BYB") == 0){
printf("L");
} if(strcmp(buffer, "pyo") == 0 || strcmp(buffer, "PYO") == 0 || strcmp(buffer, "byr") == 0 || strcmp(buffer, "BYR") == 0){
printf("L");
} if(strcmp(buffer, "pyg") == 0 || strcmp(buffer, "PYG") == 0 || strcmp(buffer, "pyg") == 0 || strcmp(buffer, "PYG") == 0){
printf("L");
} if(strcmp(buffer, "oyy") == 0 || strcmp(buffer, "OYY") == 0){
printf("I");
} if(strcmp(buffer, "oyp") == 0 || strcmp(buffer, "OYP") == 0 || strcmp(buffer, "ryb") == 0 || strcmp(buffer, "RYB") == 0){
printf("I");
} if(strcmp(buffer, "oyo") == 0 || strcmp(buffer, "OYO") == 0){
printf("I");
} if(strcmp(buffer, "oyg") == 0 || strcmp(buffer, "OYG") == 0){
printf(" - M - ");
} if(strcmp(buffer, "gyy") == 0 || strcmp(buffer, "GYY") == 0){
printf("V");
} if(strcmp(buffer, "gyp") == 0 || strcmp(buffer, "GYP") == 0 || strcmp(buffer, "gyb") == 0 || strcmp(buffer, "GYB") == 0){
printf("V");
} if(strcmp(buffer, "gyo") == 0 || strcmp(buffer, "GYO") == 0){
printf("V");
} if(strcmp(buffer, "gyg") == 0 || strcmp(buffer, "GYG") == 0){
printf("V");
} if(strcmp(buffer, "ypy") == 0 || strcmp(buffer, "YPY") == 0 || strcmp(buffer, "yby") == 0 || strcmp(buffer, "YBY") == 0){
printf("S");
} if(strcmp(buffer, "ypp") == 0 || strcmp(buffer, "YPP") == 0 || strcmp(buffer, "ybb") == 0 || strcmp(buffer, "YBB") == 0){
printf("S");
} if(strcmp(buffer, "ypo") == 0 || strcmp(buffer, "YPO") == 0 || strcmp(buffer, "ybr") == 0 || strcmp(buffer, "YBR") == 0){
printf("S");
} if(strcmp(buffer, "ypg") == 0 || strcmp(buffer, "YPG") == 0 || strcmp(buffer, "ybg") == 0 || strcmp(buffer, "YBG") == 0){
printf("S");
} if(strcmp(buffer, "ppy") == 0 || strcmp(buffer, "PPY") == 0 || strcmp(buffer, "bby") == 0 || strcmp(buffer, "BBY") == 0){
printf("P");
} if(strcmp(buffer, "ppp") == 0 || strcmp(buffer, "PPP") == 0 || strcmp(buffer, "bbb") == 0 || strcmp(buffer, "BBB") == 0){
printf("P");
} if(strcmp(buffer, "ppo") == 0 || strcmp(buffer, "PPO") == 0 || strcmp(buffer, "bbr") == 0 || strcmp(buffer, "BBR") == 0){
printf("P");
} if(strcmp(buffer, "ppg") == 0 || strcmp(buffer, "PPG") == 0 || strcmp(buffer, "bbg") == 0 || strcmp(buffer, "BBG") == 0){
printf("P");
} if(strcmp(buffer, "opy") == 0 || strcmp(buffer, "OPY") == 0 || strcmp(buffer, "rby") == 0 || strcmp(buffer, "RBY") == 0){
printf("T");
} if(strcmp(buffer, "opp") == 0 || strcmp(buffer, "OPP") == 0 || strcmp(buffer, "rbb") == 0 || strcmp(buffer, "RBB") == 0){
printf("T");
} if(strcmp(buffer, "opo") == 0 || strcmp(buffer, "OOO") == 0 || strcmp(buffer, "rbr") == 0 || strcmp(buffer, "RBR") == 0){
printf("T");
} if(strcmp(buffer, "opg") == 0 || strcmp(buffer, "OPG") == 0 || strcmp(buffer, "rbg") == 0 || strcmp(buffer, "RBG") == 0){
printf("T");
} if(strcmp(buffer, "gpy") == 0 || strcmp(buffer, "GPY") == 0 || strcmp(buffer, "gby") == 0 || strcmp(buffer, "GBY") == 0){
printf("A");
} if(strcmp(buffer, "gpp") == 0 || strcmp(buffer, "GPP") == 0 || strcmp(buffer, "gbb") == 0 || strcmp(buffer, "GBB") == 0){
printf("A");
} if(strcmp(buffer, "gpo") == 0 || strcmp(buffer, "GPO") == 0 || strcmp(buffer, "gbr") == 0 || strcmp(buffer, "GBR") == 0){
printf("A");
} if(strcmp(buffer, "gpg") == 0 || strcmp(buffer, "GPG") == 0 || strcmp(buffer, "gbg") == 0 || strcmp(buffer, "GBG") == 0){
printf("A");
} if(strcmp(buffer, "yoy") == 0 || strcmp(buffer, "YOY") == 0){
printf("Y");
} if(strcmp(buffer, "yop") == 0 || strcmp(buffer, "YOP") == 0 || strcmp(buffer, "yrb") == 0 || strcmp(buffer, "YRB") == 0){
printf("Y");
} if(strcmp(buffer, "yoo") == 0 || strcmp(buffer, "YOO") == 0){
printf(" STOP ");
} if(strcmp(buffer, "yog") == 0 || strcmp(buffer, "YOG") == 0){
printf(" STOP ");
} if(strcmp(buffer, "poy") == 0 || strcmp(buffer, "POY") == 0 || strcmp(buffer, "bry") == 0 || strcmp(buffer, "BRY") == 0){
printf("H");
} if(strcmp(buffer, "pop") == 0 || strcmp(buffer, "POP") == 0 || strcmp(buffer, "brb") == 0 || strcmp(buffer, "BRB") == 0){
printf("H");
} if(strcmp(buffer, "poo") == 0 || strcmp(buffer, "POO") == 0 || strcmp(buffer, "brr") == 0 || strcmp(buffer, "BRR") == 0){
printf("Q");
} if(strcmp(buffer, "pog") == 0 || strcmp(buffer, "POG") == 0 || strcmp(buffer, "brg") == 0 || strcmp(buffer, "BRG") == 0){
printf("Q");
} if(strcmp(buffer, "ooy") == 0 || strcmp(buffer, "OOY") == 0){
printf("N");
} if(strcmp(buffer, "oop") == 0 || strcmp(buffer, "OOP") == 0 || strcmp(buffer, "rrb") == 0 || strcmp(buffer, "RRB") == 0){
printf("N");
} if(strcmp(buffer, "ooo") == 0 || strcmp(buffer, "OOO") == 0){
printf("K");
} if(strcmp(buffer, "oog") == 0 || strcmp(buffer, "OOG") == 0){
printf("K");
} if(strcmp(buffer, "goy") == 0 || strcmp(buffer, "GOY") == 0){
printf("D");
} if(strcmp(buffer, "gop") == 0 || strcmp(buffer, "GOP") == 0 || strcmp(buffer, "grb") == 0 || strcmp(buffer, "GRB") == 0){
printf("D");
} if(strcmp(buffer, "goo") == 0 || strcmp(buffer, "GOO") == 0){
printf("E");
} if(strcmp(buffer, "gog") == 0 || strcmp(buffer, "GOG") == 0){
printf("E");
} if(strcmp(buffer, "ygy") == 0 || strcmp(buffer, "YGY") == 0){
printf("C");
} if(strcmp(buffer, "ygp") == 0 || strcmp(buffer, "YGP") == 0 || strcmp(buffer, "ygb") == 0 || strcmp(buffer, "YGB") == 0){
printf("C");
} if(strcmp(buffer, "ygo") == 0 || strcmp(buffer, "YGO") == 0){
printf(" STOP ");
} if(strcmp(buffer, "ygg") == 0 || strcmp(buffer, "YGG") == 0){
printf("W");
} if(strcmp(buffer, "pgy") == 0 || strcmp(buffer, "PGY") == 0 || strcmp(buffer, "bgy") == 0 || strcmp(buffer, "BGY") == 0){
printf("R");
} if(strcmp(buffer, "pgp") == 0 || strcmp(buffer, "PGP") == 0 || strcmp(buffer, "bgb") == 0 || strcmp(buffer, "BGB") == 0){
printf("R");
} if(strcmp(buffer, "pgo") == 0 || strcmp(buffer, "PGO") == 0 || strcmp(buffer, "bgr") == 0 || strcmp(buffer, "BGR") == 0){
printf("R");
} if(strcmp(buffer, "pgg") == 0 || strcmp(buffer, "PGG") == 0 || strcmp(buffer, "bgg") == 0 || strcmp(buffer, "BGG") == 0){
printf("R");
} if(strcmp(buffer, "ogy") == 0 || strcmp(buffer, "OGY") == 0){
printf("S");
} if(strcmp(buffer, "ogp") == 0 || strcmp(buffer, "OGP") == 0 || strcmp(buffer, "rgb") == 0 || strcmp(buffer, "RGB") == 0){
printf("S");
} if(strcmp(buffer, "ogo") == 0 || strcmp(buffer, "OGO") == 0){
printf("R");
} if(strcmp(buffer, "ogg") == 0 || strcmp(buffer, "OGG") == 0){
printf("R");
} if(strcmp(buffer, "ggy") == 0 || strcmp(buffer, "GGY") == 0){
printf("G");
} if(strcmp(buffer, "ggp") == 0 || strcmp(buffer, "GGP") == 0 || strcmp(buffer, "ggb") == 0 || strcmp(buffer, "GGB") == 0){
printf("G");
} if(strcmp(buffer, "ggo") == 0 || strcmp(buffer, "GGO") == 0){
printf("G");
} if(strcmp(buffer, "ggg") == 0 || strcmp(buffer, "GGG") == 0){
printf("G");
} else{
printf(" ");
}
}
printf("\n");
}

void deHex(char *string){
char buffer[5];
int i = 0;

while(string[i] != '\0'){
buffer[0] = string[i];
i++;
buffer[1] = string[i];
i++;
buffer[2] = string[i];
i++;
buffer[3] = string[i];
buffer[4] = '\0';
i+=2;

if(strcmp(buffer, "0000") == 0){
printf("0");
} else if(strcmp(buffer, "0001") == 0){
printf("1");
} else if(strcmp(buffer, "0010") == 0){
printf("2");
} else if(strcmp(buffer, "0011") == 0){
printf("3");
} else if(strcmp(buffer, "0100") == 0){
printf("4");
} else if(strcmp(buffer, "0101") == 0){
printf("5");
} else if(strcmp(buffer, "0110") == 0){
printf("6");
} else if(strcmp(buffer, "0111") == 0){
printf("7");
} else if(strcmp(buffer, "1000") == 0){
printf("8");
} else if(strcmp(buffer, "1001") == 0){
printf("9");
} else if(strcmp(buffer, "1010") == 0){
printf("A");
} else if(strcmp(buffer, "1011") == 0){
printf("B");
} else if(strcmp(buffer, "1100") == 0){
printf("C");
} else if(strcmp(buffer, "1101") == 0){
;printf("D");
} else if(strcmp(buffer, "1110") == 0){
printf("E");
} else if(strcmp(buffer, "1111") == 0){
printf("F");
} else{
printf(" ");
}
}
printf("\n");
}

void debacon(char *string, int btype){
char buffer[6];
int i = 0;

while(string[i] != '\0'){

buffer[0] = string[i];
i++;
buffer[1] = string[i];
i++;
buffer[2] = string[i];
i++;
buffer[3] = string[i];
i++;
buffer[4] = string[i];
buffer[5] = '\0';
i+=2;

if(btype == 0){
if(strcmp(buffer, "00000") == 0){
printf("A");
} else if(strcmp(buffer, "00001") == 0){
printf("B");
} else if(strcmp(buffer, "00010") == 0){
printf("C");
} else if(strcmp(buffer, "00011") == 0){
printf("D");
} else if(strcmp(buffer, "00100") == 0){
printf("E");
} else if(strcmp(buffer, "00101") == 0){
printf("F");
} else if(strcmp(buffer, "00110") == 0){
printf("G");
} else if(strcmp(buffer, "00111") == 0){
printf("H");
} else if(strcmp(buffer, "01000") == 0){
printf("J");
} else if(strcmp(buffer, "01001") == 0){
printf("K");
} else if(strcmp(buffer, "01010") == 0){
printf("L");
} else if(strcmp(buffer, "01011") == 0){
printf("M");
} else if(strcmp(buffer, "01100") == 0){
printf("N");
} else if(strcmp(buffer, "01101") == 0){
printf("O");
} else if(strcmp(buffer, "01110") == 0){
printf("P");
} else if(strcmp(buffer, "01111") == 0){
printf("Q");
} else if(strcmp(buffer, "10000") == 0){
printf("R");
; } else if(strcmp(buffer, "10001") == 0){
printf("S");
} else if(strcmp(buffer, "10010") == 0){
printf("T");
} else if(strcmp(buffer, "10011") == 0){
printf("V");
} else if(strcmp(buffer, "10100") == 0){
printf("W");
} else if(strcmp(buffer, "10101") == 0){
printf("X");
} else if(strcmp(buffer, "10110") == 0){
printf("Y");
} else if(strcmp(buffer, "10111") == 0){
printf("Z");
} else{
printf(" ");
}
}
if(btype == 1){
if(strcmp(buffer, "00000") == 0){
printf("A");
} else if(strcmp(buffer, "00001") == 0){
printf("B");
} else if(strcmp(buffer, "00010") == 0){
printf("C");
} else if(strcmp(buffer, "00011") == 0){
printf("D");
} else if(strcmp(buffer, "00100") == 0){
printf("E");
} else if(strcmp(buffer, "00101") == 0){
printf("F");
} else if(strcmp(buffer, "00110") == 0){
printf("G");
} else if(strcmp(buffer, "00111") == 0){
printf("H");
} else if(strcmp(buffer, "01000") == 0){
printf("I");
} else if(strcmp(buffer, "01001") == 0){
printf("J");
} else if(strcmp(buffer, "01010") == 0){
printf("K");
} else if(strcmp(buffer, "01011") == 0){
printf("L");
} else if(strcmp(buffer, "01100") == 0){
printf("M");
} else if(strcmp(buffer, "01101") == 0){
printf("N");
} else if(strcmp(buffer, "01110") == 0){
printf("O");
} else if(strcmp(buffer, "01111") == 0){
printf("P");
} else if(strcmp(buffer, "10000") == 0){
printf("Q");
} else if(strcmp(buffer, "10001") == 0){
printf("R");
} else if(strcmp(buffer, "10010") == 0){
printf("S");
} else if(strcmp(buffer, "10011") == 0){
printf("T");
} else if(strcmp(buffer, "10100") == 0){
printf("U");
} else if(strcmp(buffer, "10101") == 0){
printf("V");
} else if(strcmp(buffer, "10110") == 0){
printf("W");
} else if(strcmp(buffer, "10111") == 0){
printf("X");
} else if(strcmp(buffer, "11000") == 0){
printf("Y");
} else if(strcmp(buffer, "11001") == 0){
printf("Z");
} else{
printf(" ");
}
}
}
printf("\n");
}

void divideString(char *string, int n){
int size = strlen(string);
int i = 1;
int j = 1;
char buffer[1024];

strcpy(buffer,string);
string[0] = buffer[0];

for(i = 1; j < size; i++){
if(j%n == 0){
string[i] = ' ';
i++;
}
string[i] = buffer[j];
j++;
}
string[i] = '\0';
}

char* normalize(char* string, int nflag){
char *i;
switch(nflag){
case 0:
for(i=string; *i; i++){
if(*i == 'y' || *i == 'Y'){
*i = '1';
} else if(*i == 'o' || *i == 'O'){
*i = '0';
} else if(*i == 'g' || *i == 'G'){
*i = '1';
} else if(*i == 'p' || *i == 'P' || *i == 'b' || *i == 'B'){
*i = '0';
} else if(*i == '\n'){
*i = '\0';
}
}
return string;
case 1:
for(i=string; *i; i++){
if(*i == 'y' || *i == 'Y'){
*i = '0';
} else if(*i == 'o' || *i == 'O'){
*i == '1';
} else if(*i == 'g' || *i == 'G'){
*i = '1';
} else if(*i == 'p' || *i == 'P' || *i == 'b' || *i == 'B'){
*i = '0';
} else if(*i == '\n'){
*i == '\0';
}
}
return string;
case 2:
for(i=string; *i; i++){
if(*i == 'y' || *i == 'Y'){
*i = '1';
} else if(*i == 'o' || *i == 'O'){
*i = '0';
} else if(*i == 'g' || *i == 'G'){
*i == '0';
} else if(*i == 'p' || *i == 'P' || *i == 'b' || *i == 'B'){
*i == '1';
} else if(*i == '\n'){
*i = '\0';
}
}
return string;
case 3:
for(i=string; *i; i++){
if(*i == 'y' || *i == 'Y'){
*i = '0';
} else if(*i == 'o' || *i == 'O'){
*i = '1';
} else if(*i == 'g' || *i == 'G'){
*i = '0';
} else if(*i == 'p' || *i == 'P' || *i == 'b' || *i == 'B'){
*i = '1';
} else if(*i == '\n'){
*i = '\0';
}
}
return string;
; case 8:
for(i=string; *i; i++){
if(*i == '\n'){
*i = '\0';
}
}
return string;
default:
printf("\nERROR: Could not normalize stirng\n");
return string;
}
}

int getlines(FILE* stream, char** line, ssize_t* nread, int* ntot, size_t len){
int i = 0;
for(i = 0; i < 16; i++){
nread[i] = getline(&line[i], &len, stream);
if(nread[i] == -1){
break;
}
*ntot += nread[i];
}

return i;
}

void clean(char* string){
char *nospace = string;
char *temp = string;

        if(verbose == 1){
        printf("\nRemoving Spaces\n");
}
while(*temp != 0){
*nospace = *temp++;
if(*nospace != ' '){
nospace++;
}
}
*nospace = 0;
}

void shift(char* string){
char *nospace = string;
char *temp = string;
char buffer[1024];

char t;
int i = 0;
int size;

if(verbose == 1){
printf("\nRemoving Spaces\n");
}
while(*temp != 0){
*nospace = *temp++;
if(*nospace != ' '){
nospace++;
}
}
*nospace = 0;
if(verbose == 1){
printf("\n%s\n", string);
printf("\nShifting String\n");
}
strcpy(buffer, string);
if(verbose == 1){
printf("Buffer: \n%s\n\n", buffer);
}
t = string[0];
size = strlen(string);
for(i = 0; i < (size-1); i++){
string[i] = buffer[i+1];
}
string[i] = t;
string[i+1] = '\0';
if(verbose == 1){
printf("%s\n", string);
}
}