why error while the number is very big ?

Code:

---

char *pa[12];
char ........;

void append(char s[],char str[], uint32_t n)
{
    int i = 0;
    while(str[i] != '\0')
    {
                  s[n++] = str[i];
                  i++;
    }
}

void substring(char *s,char *r,uint32_t st,int len)
{
    int i;
    //char *p;
    for(i = 0; i < len; i++)
    {
          s = s+st;
          *r++ = *s++;
          //r[i] = s[i+st];
          //puts(r);
          //s++;
    }
    *r = '\0';
    //puts(r);
}
//[13] read2genome: read genome into memory or pointer array[12]
void read2genome(char *pa[12],char *input)
{
    FILE *fp = fopen(input,"r");
    extern char ........;
   
    while(! feof(fp))
    {
            char line[80];//temporarily store line content
            int i = 0;
            unsigned long int len;
            //char tmp[80];
            //fgets(tmp,fp);
            fscanf(fp,"%s",line);
           
            if(line[0] == '>')
            {
                        i++;
                        len = 0;
                        ss = (char *) malloc(50000000);
                        pa[i] = ss;
                        puts(line);
            }else{
                  if(line[0] == 'A' || line[0] == 'C' || line[0] == 'G' || line[0] == 'T')
                  {
                             
                              append(ss,line,len);
                              len = strlen(line)+len;
                  }
            }
    }
    fclose(fp);
}

---

Code:

---

int main(int argc,char *argv[])
{
    read2genome(pa,argv[2]);
    substring(pa[1],ss,6553500,12);
    return 0;
}

---

result :
error

the size of source file is very big
why error while the number is very big ?

>>ss = (char *) malloc(50000000);
Oh my goodness. You don't need that much memory. That's about 48 MB.

And I'm guessing that, if the source file is too big, you simply run out of memory.

And then goes the usual line: post the smallest simplest program that displays the problem.

Quote:

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Originally Posted by Elysia

>>ss = (char *) malloc(50000000);
Oh my goodness. You don't need that much memory. That's about 48 MB.

And I'm guessing that, if the source file is too big, you simply run out of memory.

And then goes the usual line: post the smallest simplest program that displays the problem.

---

Maybe the OP really does need that, whose to say? The one really bad thing about that, however, is the retval of malloc() was NOT checked.

EDIT: Oh, and another thing: If you are going to request that much memory it is best to keep in in PAGE_SIZE (usually a multiple of 4096).

Quote:

---

Originally Posted by Kennedy

Maybe the OP really does need that, whose to say? The one really bad thing about that, however, is the retval of malloc() was NOT checked.

---

I question that, seriously, because it's allocated once for each row. And if the file is 1000 rows, are you going to allocate 46 GB then?

Quote:

---

Originally Posted by Elysia

I question that, seriously, because it's allocated once for each row. And if the file 1000 rows, are you going to allocate 46 GB then?

---

I gotta start reading all the code, huh. . . didn't catch that one.

hey, that'd also be a memory leak.

Ah yes, but the current code uses fscanf to read a... string. In a buffer 80 chars long. No wonder the code fails miserably. This is very prone to buffer overruns.
SourceForge.net: Buffer overrun - cpwiki
SourceForge.net: Scanf woes - cpwiki
Stick with fgets instead.

read source file into memory is correct;
error occurs in as follow line:

Code:

---

substring(pa[1],ss,6553500,12);

---

if I use as follows code

Code:

---

substring(pa[1],ss,655350,12);

---

This program is correct!

Probably not relate to your problems but I thought I'd point out some things...

#1.

Code:

---

while(!feof(fp))
{
    char line[80];//temporarily store line content
    int i = 0;
    unsigned long int len;
    //char tmp[80];
    //fgets(tmp,fp);
    fscanf(fp,"%s",line);

---

This method of controlling a loop is often done wrong as is the case here, rarely is it ever done correctly. The problem is that the flag that says you are at the end of the file only gets set after you attempt to read past the end of the file. When you read and process the last line of data from the file, feof is still false, you are at the end of file having read the last line but the indicator is still false. Because of this you'll enter your while loop one last time and attempt the read again (calling fscanf) which will fail - although this time it will set the end-of-file flag to true - leaving the buffer unchanged from the previously correct read. The effect of all this is that the last line of data will essentially be processed twice, something I'm guessing is not what you want to have happen in your program.

The 'better' way to handle this is to make the read operation a part of the while loops conditional check. In this case, the return value of the fscanf call can be checked to make sure data was read (or not). If not, the loop is never entered and no processing of bad data can take place. If the read is successful then the loop is entered and processed.

Code:

---

char line[80];//temporarily store line content

...

while(1 == fscanf(fp,"%s",line))
{
    int i = 0;
    unsigned long int len;
    ...

---

#2.

Code:

---

ss = (char *) malloc(...);

---

You shouldn't cast the return value from the malloc call in C.