Program Bugs with large sequences (C) [closed] - c

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I am trying to code the Waterman algorithm in C.
Now when the length of the sequence exceeds 35 the program just lags.
I have no idea where to start looking, tried but got nothing worked out.
Here's the code:
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
// Max Function Prototype.
int maxfunction(int, int);
// Prototype of the random Sequences generator Function.
void gen_random(char *, const int);
int main(int argc, char *argv[]) {
// Looping variable and Sequences.
int i = 0, j = 0, k = 0;
char *X, *Y;
int length1, length2;
// Time Variables.
time_t beginning_time, end_time;
// Getting lengths of sequences
printf("Please provide the length of the first Sequence\n");
scanf("%d", &length1);
printf("Please provide the length of the second Sequence\n");
scanf("%d", &length2);
X = (char*)malloc(sizeof(char) * length1);
Y = (char*)malloc(sizeof(char) * length2);
int m = length1 + 1;
int n = length2 + 1;
int L[m][n];
int backtracking[m + n];
gen_random(X, length1);
gen_random(Y, length2);
printf("First Sequence\n");
for (i = 0; i < length1; i++) {
printf("%c\n", X[i]);
}
printf("\nSecond Sequence\n");
for (i = 0; i < length2; i++) {
printf("%c\n", Y[i]);
}
// Time calculation beginning.
beginning_time = clock();
// Main Part--Core of the algorithm.
for (i = 0; i <= m; i++) {
for (j = 0; j <= n; j++) {
if (i == 0 || j == 0) {
L[i][j] = 0;
} else
if (X[i-1] == Y[j-1]) {
L[i][j] = L[i-1][j-1] + 1;
backtracking[i] = L[i-1][j-1];
} else {
L[i][j] = maxfunction(L[i-1][j], L[i][j-1]);
backtracking[i] = maxfunction(L[i-1][j], L[i][j-1]);
}
}
}
// End time calculation.
end_time = clock();
for (i = 0; i < m; i++) {
printf(" ( ");
for (j = 0; j < n; j++) {
printf("%d ", L[i][j]);
}
printf(")\n");
}
// Printing out the result of backtracking.
printf("\n");
for (k = 0; k < m; k++) {
printf("%d\n", backtracking[k]);
}
printf("Consumed time: %lf", (double)(end_time - beginning_time));
return 0;
}
// Max Function.
int maxfunction(int a, int b) {
if (a > b) {
return a;
} else {
return b;
}
}
// Random Sequence Generator Function.
void gen_random(char *s, const int len) {
int i = 0;
static const char alphanum[] = "ACGT";
for (i = 0; i < len; ++i) {
s[i] = alphanum[rand() % (sizeof(alphanum) - 1)];
}
s[len] = 0;
}

Answer 1

Since you null terminate the sequence in gen_random with s[len] = 0;, you should allocate 1 more byte for each sequence:
X = malloc(sizeof(*X) * (length1 + 1));
Y = malloc(sizeof(*Y) * (length2 + 1));
But since you define variable length arrays for other variables, you might as well define these as:
char X[length1 + 1], Y[length2 + 1];
Yet something else is causing a crash on my laptop: your nested loops iterate from i = 0 to i <= m, and j = 0 to j <= n. That's one step too many, you index out of bounds into L.
Here is a corrected version:
for (i = 0; i < m; i++) {
for (j = 0; j < n; j++) {
The resulting code executes very quickly, its complexity is O(m*n) in both time and space, but m and n are reasonably small at 35. It runs in less than 50ms for 1000 x 1000.
Whether it implements Smith-Waterman's algorithm correctly is another question.