Here's a reasonably fast one.

# include <stdio.h>
# include <stdlib.h>
# include <errno.h>

int main(int argc, char **argv) {
    if (argc != 3) {
        fprintf(stderr, "Usage: %s <input_file> <comparison_file>\n", 
+argv[0]);
        exit(1);
    }

    FILE *in_file = fopen(argv[1], "r");
    if (in_file == NULL) {
        perror(argv[1]); exit(1);
    }
    FILE *cmp_file = fopen(argv[2], "r");
    if (cmp_file == NULL) {
        perror(argv[2]); exit(1);
    }
    
    for (;;) {
        char cmp = fgetc(cmp_file);
        char inp = fgetc(in_file);

        if (cmp == '-') {
            continue;
        }
        if (cmp == EOF || inp == EOF) {
            break;
        }

        putchar(inp);
    }

    fclose(in_file);
    fclose(cmp_file);

    exit(0);
}
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Compile:

gcc -O3 tr_big_string.c -o tr_big_string
[download]

Usage:

./tr_big_string ./big_string_file ./comparison_file
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