geinf/vcf_to_sfs.c

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

bool StartsWith(const char *a, const char *b)
{
   if(strncmp(a, b, strlen(b)) == 0) return 1;
   return 0;
}

void slice_str(const char * str, char * buffer, size_t start, size_t end)
{
    size_t j = 0;
    for ( size_t i = start; i <= end; ++i ) {
        buffer[j++] = str[i];
    }
    buffer[j] = 0;
}


# define LL 8192   /* line length maximum */

int main ( int argc, char *argv[] ){
    if ( argc < 3) {
	printf("Need 2 args!\n");
	return 1;
    }
    gzFile fp;
    char line[LL];
    char delim[] = "\t";
    fp = gzopen( argv[1], "r" );

    gzgets( fp, line, LL );
    while ( ! gzeof( fp ) ){
	int k = 0;
	if ( StartsWith(line, "##") || ( StartsWith(line, "#") ) || (strstr(line, "./.:.") != NULL)){
	    gzgets( fp, line, LL );
	    continue;
	}
	
	char *vcf_field = strtok(line, delim);
	while(vcf_field != NULL){
	    k++;
	    if (k > 9) {
		const size_t len = strlen(vcf_field);
		char buffer[len + 1];
		//printf("'%s'\n", ptr);
		slice_str(vcf_field, buffer, 0, 0);
		printf("%s      ", buffer);
	    }
	    vcf_field = strtok(NULL, delim);
	}
	// printf("%s", line );
	// loads the next line
	gzgets( fp, line, LL );
    }

    gzclose( fp );
    return 0;
}