input files in C

Code implements the dynamic programming solution for global pairwise alignment of two sequences. Trying to perform a semi-global alignment between the SARS-CoV-2 reference genome and the first read in the Nanopore sample. The length of the reference genome is 29903 base pairs and the length of the first Nanopore read is 1246 base pairs. When I run the following code, I get this message in my terminal:

Usage: align < input file >

How do I add the necessary files to the code. The file names are SARS-CoV-2 reference genome.txt and Nanopore.txt, where A = SARS-CoV-2 reference genome.txt file and B = Nanopore.txt file

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

#define GAP -2
#define MATCH 5
#define MISMATCH -3

#define MAXLENGTH_A 29904
#define MAXLENGTH_B 1247

int max(int A, int B, int C)
{
    if (A>=B && A>=C) return A;
    else if (B>=A && B>=C) return B;
    else return C;
}

char Tmax(int A, int B, int C)
{
    if (A>B && A>C) return 'D';
    else if (B>A && B>C) return 'L';
    else return 'U';
}

int m(char p, char q)
{
    if (p==q) return MATCH;
    else return MISMATCH;
}

void append(char *st,int L,char c)
{
     int i;
     for (i=L;i>0;i--)
         st[i]=st[i-1];
     st[L+1] = '\0';
     st[0] = c;
}

int main(int argc, char **argv)
{
    FILE *fp;
    
    char A[1000];
    char B[1000];
    char RA[1000];
    char RM[1000];
    char RB[1000];
    int N,M,L;
    
    int i,j;
    
    //int S[MAXLENGTH_A][MAXLENGTH_B];
    //char T[MAXLENGTH_A][MAXLENGTH_B];
    int **S;
    char **T;
    S = (int**)malloc(sizeof(int*)*MAXLENGTH_A);
    for (int i = 0; i<29904; i++)
        S[i] = (int*)malloc(sizeof(int)*MAXLENGTH_B);
    T = (char**)malloc(sizeof(char*)*MAXLENGTH_A);
    for (int i = 0; i<29904; i++)
        T[i] = (char*)malloc(sizeof(char)*MAXLENGTH_B);
    
    if (argc!=2)
    {
                printf("Usage: align <input file>\n");
                exit(1);
    }
    
    fp = fopen(argv[2],"r");
    
    if (fp==NULL)
    {
                  printf("input file not found.\n");
                  exit(1);
    }
    fscanf(fp,"%s",A);
    fscanf(fp,"%s",B);
    
    printf("Sequence A: %s\n",A);
    printf("Sequence B: %s\n",B);
    
    N = strlen(A);
    M = strlen(B);
    S[0][0] = 0;
    T[0][0] = 'D';
    
    // initialize first column
    for (i=0;i<=N;i++)
    {
        S[i][0] = GAP*i;
        T[i][0] = 'U';
    }
    
    //initialize the firt row
    for (i=0;i<=M;i++)
    {
        S[0][i] = GAP*i;
        T[0][i] = 'L';
    }
    
    for (i=1;i<=N;i++)
        for (j=1;j<=M;j++)
        {
            S[i][j] = max(S[i-1][j-1]+m(A[i-1],B[j-1]),S[i][j-1]+GAP,S[i-1][j]+GAP);
            T[i][j] = Tmax(S[i-1][j-1]+m(A[i-1],B[j-1]),S[i][j-1]+GAP,S[i-1][j]+GAP);
        }
    
    printf("The score of the alignment is : %d\n",S[N][M]);
    
    i=N;
    j=M;
    L=0;
    RA[0]='\0';
    RB[0]='\0';
    RM[0]='\0';
    
    while (i!=0 || j!=0)
    {
          if (T[i][j]=='D')
          {
             append(RA,L,A[i-1]);
             append(RB,L,B[j-1]);
             if (A[i-1]==B[j-1]) append(RM,L,'|');
             else append(RM,L,'*');
             i--; j--;
          }
          else if (T[i][j]=='L')
          {
             append(RA,L,'-');
             append(RB,L,B[j-1]);
             append(RM,L,' ');
             j--;
          }
          else if (T[i][j]=='U')
          {
             append(RA,L,A[i-1]);
             append(RB,L,'-');
             append(RM,L,' ');
             i--;
          }
          
          L++;
          
    }
    
    printf("%s\n",RA);
    printf("%s\n",RM);
    printf("%s\n",RB);
}