I am having trouble debugging my implementation of Vigenere's cipher in C. The error arises when using file input (-f flag) where the file contains fewer than 6 chars (+ 1 EOF), it spits out some number of random characters as well as the expected input and I cannot figure out why this is, although I suspect it has something to do with the second part of my question which is, when using fread(), I noticed that this
if( fread(fcontents, fsize, sizeof(char), file) != 1 ) {...}
will run with no issues, whereas this
if( fread(fcontents, sizeof(char), fsize, file) != 1 ) {...}
doesn't work (i.e. causes fread() to return 1 and trigger the error handling code beneath it), which I would expect to be the other way around according to answers from here, but I may just be misinterpreting something.
My complete code is as follows:
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#include <unistd.h>
#define ENC 0 //Encrypt mode
#define DEC 1 //Decrypt mode
#define INP 0 //Commandline input mode
#define FLE 1 //File input mode
typedef struct {
    char *password;
    char *file_name;
    char *input;
    int edmode;
    int ifmode;
} options;
void string_clean(char *source)
{
    char *i = source;
    char *j = source;
    while(*j != 0) {
        *i = *j++;
        if( *i != ' ' && (isupper(*i) || islower(*i)) )
            i++;
    }
    *i = 0;
}
char *ftostr(char *file_name) //Takes a file name as input and returns a char* to the files contents, returns NULL pointer on faliure. Allocated string must be freed after use by parent function to prevent memory leaks.
{
    FILE *file;
    long int fsize;
    char *fcontents;
    if( !(file = fopen(file_name, "r")) ) {
        fprintf(stderr, "Error opening file \"%s\"!\n", file_name);
        return NULL;
    }
    fseek(file, 0L, SEEK_END);
    fsize = ftell(file);
    rewind(file);
    if( !(fcontents = malloc((fsize + 1) * sizeof(char))) ) {
        fclose(file);
        fprintf(stderr, "Error allocating memory!");
        return NULL;
    }
    if( fread(fcontents, fsize, sizeof(char), file) != 1 ) { //suspected buggy line
        fclose(file);
        free(fcontents);
        fprintf(stderr, "Error copying file to memory!\n");
        return NULL;
    }
    fclose(file);
    return fcontents;
}
options parse_opts(int argc, char *argv[])
{
    int c;
    options args;
    args.edmode     = ENC; //enable encrypt mode by default
    args.ifmode     = INP; //enable commandline input mode by default
    args.file_name  = NULL;
    args.password   = NULL;
    args.input      = NULL;
    opterr          = 0;
    while((c = getopt(argc, argv, "dep:i:f:")) != -1) {
        switch(c) {
            case 'e':
                args.edmode     = ENC;
                break;
            case 'd':
                args.edmode     = DEC;
                break;
            case 'p':
                args.password   = optarg;
                break;
            case 'i':
                args.input      = optarg;
                args.ifmode     = INP;
                break;
            case 'f':
                args.file_name  = optarg;
                args.ifmode     = FLE;
                break;
            case '?':
                if(optopt == 'f' || optopt == 'p' || optopt == 'i')
                    fprintf(stderr, "Option -%c requires an argument.\n", optopt);
                else if(isprint(optopt))
                    fprintf(stderr, "Unknown option `-%c'.\n", optopt);
                else
                    fprintf(stderr, "Unknown option character `\\x%x'.\n", optopt);
                fprintf(stderr, "Usage: %s (-f file_name || -i input) -p password [options]\n"
                                "Optional: -e -d\n", argv[0]);
                exit(-1);
        }
    }
    return args;
}
char *vigenere_dec(char cipher_text[], char cipher[])
{
    char *plain_text;
    string_clean(cipher_text);
    string_clean(cipher);
    int plain_text_len = strlen(cipher_text);
    int cipher_len = strlen(cipher);
    if( !(plain_text = malloc((plain_text_len + 1) * sizeof(char))) )
        return 0;
    for(int i = 0; i < cipher_len; i++) {
        if(isupper(cipher[i]))
            cipher[i] -= 'A';
        else if(islower(cipher[i]))
            cipher[i] -= 'a';
    }
    for(int i = 0, j = 0; i < plain_text_len; i++, j++) {
        if(j == cipher_len)
            j = 0;
        if(isupper(cipher_text[i]))
            cipher_text[i] -= 'A';
        else if(islower(cipher_text[i]))
            cipher_text[i] -= 'a';
        plain_text[i] = ((cipher_text[i] - cipher[j]) % 26);
        if(plain_text[i] < 0)
            plain_text[i] += 26;
        plain_text[i] += 'A';
    }
    return plain_text;
}
char *vigenere_enc(char plain[], char cipher[])
{
    char *cipher_text;
    string_clean(plain);
    string_clean(cipher);
    int plain_len   = strlen(plain);
    int cipher_len  = strlen(cipher);
    if(plain_len == 0 || cipher_len == 0)
        return NULL;
    if( !(cipher_text = malloc((plain_len + 1) * sizeof(char))) )
        return NULL;
    for(int i = 0; i < cipher_len; i++) {
        if(isupper(cipher[i]))
            cipher[i] -= 'A';
        else if(islower(cipher[i]))
            cipher[i] -= 'a';
    }
    for(int i = 0, j = 0; i < plain_len; i++, j++) {
        if(j == cipher_len)
            j = 0;
        if(isupper(plain[i]))
            plain[i] -= 'A';
        else if(islower(plain[i]))
            plain[i] -= 'a';
        cipher_text[i] = ((plain[i] + cipher[j]) % 26) + 'A';
    }
    return cipher_text;
}
int main(int argc, char *argv[])
{
    options args;
    char *output_text = NULL;
    args = parse_opts(argc, argv);
    if(args.password == NULL) {
        fprintf(stderr, "Password uninitialised!\n");
        exit(-1);
    }
    if(args.input == NULL && args.file_name == NULL) {
        fprintf(stderr, "Input stream uninitialised!\n");
        exit(-1);
    }
    if(args.ifmode == INP) {
        if(args.edmode == ENC)
            output_text = vigenere_enc(args.input, args.password);
        else if(args.edmode == DEC)
            output_text = vigenere_dec(args.input, args.password);
    } else if(args.ifmode == FLE) {
        if( !(args.input = ftostr(args.file_name)) )
            return -1;
        if(args.edmode == ENC)
            output_text = vigenere_enc(args.input, args.password);
        else if(args.edmode == DEC)
            output_text = vigenere_dec(args.input, args.password);
        free(args.input);
    }
    puts(output_text);
    free(output_text);
    return 0;
}