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

#include "util/util.h"
#include "qidx.h"

void qidx_die_err(qidx_err_t err) {
	char const * errstr = qidx_strerr(err);
	if(qidx_errno(err)) {
		die_errno("err: %s", errstr);
	} else {
		die("err: %s", errstr);
	}
}

void die_usage(char const * prog) {
	err("%s {create,search}", prog);
	err("   create [bamfile] [indexfile]");
	die("   search [index] [bamfile] [read]");
}

int main(int argc, char ** argv) {

	if(!argc) return 1;

	if(argc < 3) die_usage(argv[0]);

	char const * type = argv[1];
	qidx_err_t err;
	char const * prog = argv[0];

	if(strcmp(type, "create") == 0) {
		int option;
		uint32_t n_buckets = 0;
		uint32_t max_bucket_size = 1 << 18;

		while((option = getopt(argc, argv, ":b:s:")) != -1) {
			switch(option) {
				case 'b':
					if(1 != sscanf(optarg, "%u", &n_buckets)) {
						die("could not parse -b");
					}
					break;
				case 's':
					if(1 != sscanf(optarg, "%u", &max_bucket_size)) {
						die("could not parse -s");
					}
					break;
				case ':':
					die("option needs a value");
				case '?':
					die("Unknown option %c", optopt);
					break;
			}
		}

		if(argc - optind != 3) die_usage(prog);

		char const * bamfile = argv[optind + 1];
		char const * indexfile = argv[optind + 2];

		if((err = qidx_create_index1(bamfile,
					indexfile, n_buckets, max_bucket_size))) {
			qidx_die_err(err);
		}

	} else if (strcmp(type, "search") == 0) {
		if(argc != 5) die_usage(prog);

		char const * indexfile = argv[2];
		char const * bamfile = argv[3];
		char const * qname = argv[4];

		if((err = qidx_search_index(indexfile, bamfile, qname))) {
			qidx_die_err(err);
		}

	} else {
		die_usage(argv[0]);
	}

}