test_bz.c

#include <bzlib.h>
#include <zlib.h>
#include <stdio.h>
#include <stdlib.h>

typedef struct zfile_s {
	int is_bz;
	gzFile fpz;
	FILE *fp; // for bzip2
	BZFILE *fpbz;
} *zfile_t;

static inline ssize_t zfile_read(zfile_t fp, void *buf, size_t len)
{
	if (fp->is_bz) {
		int err;
		return BZ2_bzRead(&err, fp->fpbz, buf, len);
	} else return gzread(fp->fpz, buf, len);
}

zfile_t zfile_open(const char *fn, int is_bz)
{
	zfile_t fp;
	fp = calloc(1, sizeof(struct zfile_s));
	if (is_bz) {
		int err;
		fp->is_bz = 1;
		fp->fp = fopen(fn, "rb");
		fp->fpbz = BZ2_bzReadOpen(&err, fp->fp, 0, 0, 0, 0);
	} else fp->fpz = fn? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
	return fp;
}

void zfile_close(zfile_t fp)
{
	if (fp->is_bz) {
		int err;
		BZ2_bzReadClose(&err, fp->fpbz);
		fclose(fp->fp);
	} else gzclose(fp->fpz);
	free(fp);
}

#include "kseq.h"
KSEQ_INIT(zfile_t, zfile_read)

#include <unistd.h>

int main(int argc, char *argv[])
{
	zfile_t fp;
	kseq_t *seq;
	int c, l, is_bz = 0;
	while ((c = getopt(argc, argv, "b")) >= 0)
		if (c == 'b') is_bz = 1;
	if (argc == optind) {
		fprintf(stderr, "Usage: %s [-b] <in.fasta>\n", argv[0]);
		return 1;
	}
	fp = zfile_open(argv[optind], is_bz);
	seq = kseq_init(fp);
	while ((l = kseq_read(seq)) >= 0) {
		printf("name: %s\n", seq->name.s);
		if (seq->comment.l) printf("comment: %s\n", seq->comment.s);
		printf("seq: %s\n", seq->seq.s);
		if (seq->qual.l) printf("qual: %s\n", seq->qual.s);
	}
	printf("return value: %d\n", l);
	kseq_destroy(seq);
	zfile_close(fp);
	return 0;
}