Ejemplo n.º 1
0
int fai_build(const char *fn)
{
	char *str;
	RAZF *rz;
	FILE *fp;
	faidx_t *fai;
	str = (char*)calloc(strlen(fn) + 5, 1);
	sprintf(str, "%s.fai", fn);
	rz = razf_open(fn, "r");
	if (rz == 0) {
		fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
		free(str);
		return -1;
	}
	fai = fai_build_core(rz);
	razf_close(rz);
	fp = fopen(str, "wb");
	if (fp == 0) {
		fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
		fai_destroy(fai); free(str);
		return -1;
	}
	fai_save(fai, fp);
	fclose(fp);
	free(str);
	fai_destroy(fai);
	return 0;
}
Ejemplo n.º 2
0
faidx_t *fai_load(const char *fn)
{
	char *str;
	FILE *fp;
	faidx_t *fai;
	str = (char*)calloc(strlen(fn) + 5, 1);
	sprintf(str, "%s.fai", fn);

#ifdef _USE_KNETFILE
    if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
    {
        fp = download_and_open(str);
        if ( !fp )
        {
            fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
            free(str);
            return 0;
        }
    }
    else
#endif
        fp = fopen(str, "rb");
	if (fp == 0) {
		fprintf(stderr, "[fai_load] build FASTA index.\n");
		fai_build(fn);
		fp = fopen(str, "rb");
		if (fp == 0) {
			fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
			free(str);
			return 0;
		}
	}

	fai = fai_read(fp);
	fclose(fp);

	fai->rz = razf_open(fn, "rb");
	free(str);
	if (fai->rz == 0) {
		fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
		return 0;
	}
	return fai;
}
Ejemplo n.º 3
0
int main(int argc, char **argv)
{
	int c, compress, pstdout, is_forced;
	RAZF *rz;
	void *buffer;
	long start, end, size;

	compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
	while((c  = getopt(argc, argv, "cdlhfb:s:")) >= 0){
		switch(c){
		case 'h': return razf_main_usage();
		case 'd': compress = 0; break;
		case 'c': pstdout = 1; break;
		case 'l': compress = 2; break;
		case 'b': start = atol(optarg); break;
		case 's': size = atol(optarg); break;
		case 'f': is_forced = 1; break;
		}
	}
	if (size >= 0) end = start + size;
	if(end >= 0 && end < start){
		fprintf(stderr, " -- Illegal region: [%ld, %ld] --\n", start, end);
		return 1;
	}
	if(compress == 1){
		int f_src, f_dst = -1;
		if(argc > optind){
			if((f_src = open(argv[optind], O_RDONLY)) < 0){
				fprintf(stderr, " -- Cannot open file: %s --\n", argv[optind]);
				return 1;
			}
			if(pstdout){
				f_dst = fileno(stdout);
			} else {
				char *name = malloc(sizeof(strlen(argv[optind]) + 5));
				strcpy(name, argv[optind]);
				strcat(name, ".rz");
				f_dst = write_open(name, is_forced);
				if (f_dst < 0) return 1;
				free(name);
			}
		} else if(pstdout){ 
			f_src = fileno(stdin);
			f_dst = fileno(stdout);
		} else return razf_main_usage();
		rz = razf_dopen(f_dst, "w");
		buffer = malloc(WINDOW_SIZE);
		while((c = read(f_src, buffer, WINDOW_SIZE)) > 0) razf_write(rz, buffer, c);
		razf_close(rz); // f_dst will be closed here
		if (argc > optind && !pstdout) unlink(argv[optind]);
		free(buffer);
		close(f_src);
		return 0;
	} else {
		if(argc <= optind) return razf_main_usage();
		if(compress == 2){
			rz = razf_open(argv[optind], "r");
			if(rz->file_type == FILE_TYPE_RZ) {
							printf("%20s%20s%7s %s\n", "compressed", "uncompressed", "ratio", "name");
				printf("%20lld%20lld%6.1f%% %s\n", (long long)rz->end, (long long)rz->src_end, rz->end * 100.0f / rz->src_end,
					   argv[optind]);
			} else fprintf(stdout, "%s is not a regular rz file\n", argv[optind]);
		} else {
			int f_dst;
			if (argc > optind && !pstdout) {
				char *name;
				if (strstr(argv[optind], ".rz") - argv[optind] != strlen(argv[optind]) - 3) {
					printf("razip: %s: unknown suffix -- ignored\n", argv[optind]);
					return 1;
				}
				name = strdup(argv[optind]);
				name[strlen(name) - 3] = '\0';
				f_dst = write_open(name, is_forced);
				free(name);
			} else f_dst = fileno(stdout);
			rz = razf_open(argv[optind], "r");
			buffer = malloc(WINDOW_SIZE);
			razf_seek(rz, start, SEEK_SET);
			while(1){
				if(end < 0) c = razf_read(rz, buffer, WINDOW_SIZE);
				else c = razf_read(rz, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
				if(c <= 0) break;
				start += c;
				write(f_dst, buffer, c);
				if(end >= 0 && start >= end) break;
			}
			free(buffer);
			if (!pstdout) unlink(argv[optind]);
		}
		razf_close(rz);
		return 0;
	}
}