parse tab delimited standard input

stdin.c

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

/* The block below is included so that the program will compile on the macintosh, which lacks gnu's getline. Compilation produces a non-fatal warning*/
/* This code is public domain -- Will Hartung 4/9/09 -from http://stackoverflow.com/questions/735126/are-there-alternate-implementations-of-gnu-getline-interface*/
size_t getline(char **lineptr, size_t *n, FILE *stream) {
    char *bufptr = NULL;
    char *p = bufptr;
    size_t size;
    int c;
    if (lineptr == NULL) {
        return -1;
    }
    if (stream == NULL) {
        return -1;
    }
    if (n == NULL) {
        return -1;
    }
    bufptr = *lineptr;
    size = *n;
    c = fgetc(stream);
    if (c == EOF) {
        return -1;
    }
    if (bufptr == NULL) {
        bufptr = malloc(128);
        if (bufptr == NULL) {
                return -1;
        }
        size = 128;
    }
    p = bufptr;
    while(c != EOF) {
        if ((p - bufptr) > (size - 1)) {
                size = size + 128;
                bufptr = realloc(bufptr, size);
                if (bufptr == NULL) {
                        return -1;
                }
        }
        *p++ = c;
        if (c == '\n') {
                break;
        }
        c = fgetc(stream);
    }
    *p++ = '\0';
    *lineptr = bufptr;
    *n = size;
    return p - bufptr - 1;
}
/* This code is public domain -- Will Hartung 4/9/09 -from: http://stackoverflow.com/questions/735126/are-there-alternate-implementations-of-gnu-getline-interface*/
/* The block above is included so that the program will compile on the macintosh, which lacks gnu's getline*/

int main()
{
	while(1){
		if(feof( stdin ) !=0){
			break;	
		}
		int bytes_read;
		int nbytes = 100;
		char *my_string;
		my_string = (char *) malloc (nbytes + 1);
		bytes_read = getline (&my_string, &nbytes, stdin);
		if (bytes_read == -1){
			break;
		}
		else{
			int field = 0;
			char delim[] = "\t";
                       /*yes, i know should probably place these in an array*/
			char *contig;
			char *site;
			char *ref;
			char *nreads;
			char *cigar;
			char *quals;
			char *result = NULL;
			result = strtok( my_string, delim );
			while( result != NULL ){
				if (field > 5){
					break;	
				}
				if( field == 0){
					contig = result;	
				}
				if( field == 1){
					site = result;	
				}
				if( field == 2){
					ref = result;	
				}
				if( field == 3){
					nreads = result;	
				}
				if( field == 4){
					cigar = result;	
				}
				if( field == 5){
					quals = result;	
		    		printf("contig: %s\n", contig);
		    		printf("site: %s\n", site);
		    		printf("ref: %s\n", ref);
		    		printf("nreads: %s\n", nreads);
		    		printf("cigar: %s\n", cigar);
		    		printf("quals: %s\n", quals);
				}
				result = strtok( NULL, delim );
				field++;
			}
		}
	}
	return 0;
}