Problem code

#include <ctype.h>
#include <stdio.h>
#include <stdbool.h>
#include <stdlib.h>
#include <string.h>

void initializeEncryptArray(char key[], char encrypt[]);
void initializeDecryptArray(char encrypt[], char decrypt[]);
char * removeDuplicates(char word[]);
int targetFound(char charArray[], int num, char target);
void processInput(FILE *inf, FILE * outF, char substitute[]);

int main(int argc, char * argv[])
{
    int choice;
    char *ch;
    bool loop = true;
    FILE *fin, *fout;

    if (argc != 5)
    {
        printf ("Usage: cipher option key infile, outfile\n");
        printf ("Option 1 for encryption and 2 for decryption\n");
        exit(1);
    }

    choice = atoi(argv[1]);
    char *k = argv[2];

    fin = fopen(argv[3], "r");
    fout = fopen(argv[4], "w");

    if (fin ==  NULL || fout == NULL)
    {
        printf("File could not be opened\n");
        exit(1);
    }

    char encrypt[26], decrypt[26];
    initializeEncryptArray(k, encrypt);
    initializeDecryptArray(encrypt, decrypt);

    if (choice == 1){
        processInput(fin, fout, encrypt);
    }else if (choice == 2){
        processInput(fin, fout, decrypt);
    }else {
        printf ("Usage: cipher option key infile, outfile\n");
        printf ("Option 1 for encryption and 2 for decryption\n");
        exit(1);
    }

    fclose(fin);
    fclose(fout);

    return 0;
}

void initializeEncryptArray(char key[], char encrypt[])
{
    int i = 0, j = 90;

    char *endkey = removeDuplicates(key);
    printf("%s\n", endkey);

    while(endkey[i] != '\0'){
        encrypt[i] = endkey[i];
        i++;
    }

    while(j >= 65){
        if (targetFound(encrypt, i, (char)j) != 0){
            encrypt[i] = (char)j;
            i++;
        }
        j--;
    }
    printf("Finished encryption.\n");
    printf("%c\n", encrypt[0]);
}

void initializeDecryptArray(char encrypt[], char decrypt[])
{
    int i = 0, j = 0;
    while (i < 26){
        decrypt[((int)(encrypt[i]))-65] = (char) (i + 65);
        i++;
    }
}


char * removeDuplicates(char word[]){
    int i, j;
    bool match = false;

    char *result = "";
    char end[26] = "";
    for (i = 0; i < (strlen(word)+1); i++){
        if (i < strlen(word)){
            for (j = 0; j <= strlen(end); j++){
                if (end[j] == word[i]){
                    match = true;
                }
            }
            if (match != true){
                end[i] = word[i];
            }
        }else {
            end[i] = '\0';
        }
    }

    word = end;
    return word;
}

int targetFound(char charArray[], int num, char target){
    int i = 0;
    while (i <= num){
        if (charArray[i] == target){
            return 1;
        }
        i++;
    }
    return 0;
}

void processInput(FILE *inF, FILE * outF, char substitute[]){
    int parsed = 0;
    char ch;

    while ( fscanf(inF, "%s", &ch) != EOF ){
        if(isupper(ch)){
            parsed = ((char) ch) - 65;
            fprintf(outF, "%c", substitute[parsed]);
        }else if(islower(ch)){
            parsed = ((char) ch) - 97;
            fprintf(outF, "%c", substitute[parsed + 32]);
        }else {
            parsed = ch;
            fprintf(outF, "%c", substitute[parsed]);
        }
    }
}