Optimising single-delimiter string tokenisation
I tried the following change to your function. It does not use strtok. It does the tokenizing in the function itself. I got a little bit of speed up.

void split_line2(string &amp;line, input_record &amp;rec)
{
    int col = 0;
    char *start = &amp;line[0];
    char sep = ','; // Using ',' instead of '\t' for my testing.
    for ( char* iter = start; *iter != '\0'; ++iter )
    {
       if ( *iter == sep )
       {
          *iter = '\0';
          switch(++col)
          {
             case 2 : rec.sequence = start; break;
             case 4 : rec.content = start; break;
             case 9 : rec.position = atoi(start); return;
          }
          start = iter+1;
       }
    }
}


Here's the test program and results from my testing:

#include &lt;iostream&gt;
#include &lt;string&gt;
#include &lt;ctime&gt;
#include &lt;cstring&gt;

using std::string;

struct input_record
{
    string sequence;
    string content;
    unsigned int position;
};

void split_line1(string &amp;line, input_record &amp;rec)
{
    int col = 0;
    char *row = &amp;line[0];
    char *token = strtok(row, ",");
    while (token)
    {
        switch(++col)
        {
            case 2 : rec.sequence = token; break;
            case 4 : rec.content = token; break;
            case 9 : rec.position = atoi(token); return;
        }
        token = strtok(NULL, ",");
    }
}

void split_line2(string &amp;line, input_record &amp;rec)
{
    int col = 0;
    char *start = &amp;line[0];
    char sep = ',';
    for ( char* iter = start; *iter != '\0'; ++iter )
    {
       if ( *iter == sep )
       {
          *iter = '\0';
          switch(++col)
          {
             case 2 : rec.sequence = start; break;
             case 4 : rec.content = start; break;
             case 9 : rec.position = atoi(start); return;
          }
          start = iter+1;
       }
    }
}

void test1(std::string &amp;line, int n)
{
   clock_t start = clock();

   for ( int i = 0; i &lt; n; ++i )
   {
      input_record rec;
      split_line1(line, rec);
   }

   clock_t end = clock();
   std::cout &lt;&lt; "Time: " &lt;&lt; (end-start)/CLOCKS_PER_SEC &lt;&lt; std::endl;
}

void test2(std::string &amp;line, int n)
{
   clock_t start = clock();

   for ( int i = 0; i &lt; n; ++i )
   {
      input_record rec;
      split_line2(line, rec);
   }

   clock_t end = clock();
   std::cout &lt;&lt; "Time: " &lt;&lt; (end-start)/CLOCKS_PER_SEC &lt;&lt; std::endl;
}

int main(int argc, char** argv)
{
   std::string line(argv[1]);
   int n = atoi(argv[2]);
   test1(line, n);
   test2(line, n);
}


Results:


~/Stack-Overflow/cpp>>./test-507 "1,abcd,3,xyz,4,5,6,7,8,9,10,11" 50000000
Time: 3
Time: 2

~/Stack-Overflow/cpp>>./test-507 "1,abcd,3,xyz,4,5,6,7,8,9,10,11" 100000000
Time: 6
Time: 4

~/Stack-Overflow/cpp>>./test-507 "1,abcd,3,xyz,4,5,6,7,8,9,10,11" 200000000
Time: 13
Time: 9

~/Stack-Overflow/cpp>>./test-507 "1,abcd,3,xyz,4,5,6,7,8,9,10,11" 400000000
Time: 26
Time: 18


Update

If I change the struct from containing std::string to char*, there is substantial savings.

struct input_record
{
    char* sequence;
    char* content;
    unsigned int position;
};



~/Stack-Overflow/cpp>>./test-507 "1,abcd,3,xyz,4,5,6,7,8,9,10,11" 400000000
Time: 16
Time: 8


If that is an option, that will be save you a bunch of time.