static inline int32_t
tmap_refseq_supported(tmap_refseq_t *refseq)
{
int32_t i, j;
char *refseq_v = refseq->package_version->s;
char *tmap_v = PACKAGE_VERSION;
// sanity check on version names
for(i=j=0;i<strlen(refseq_v);i++) {
if('.' == refseq_v[i]) j++;
}
if(2 != j) {
tmap_error("did not find three version numbers", Exit, OutOfRange);
}
for(i=j=0;i<strlen(tmap_v);i++) {
if('.' == tmap_v[i]) j++;
}
if(2 != j) {
tmap_error("did not find three version numbers", Exit, OutOfRange);
}
// get the format ids
if(0 == strcmp(tmap_refseq_get_version_format(refseq_v), tmap_refseq_get_version_format(tmap_v))) {
return 1;
}
return 0;
}
static inline void
tmap_refseq_print_header(tmap_file_t *fp, tmap_refseq_t *refseq)
{
uint32_t i;
tmap_file_fprintf(fp, "version id:\t%llu\n", (unsigned long long int)refseq->version_id);
tmap_file_fprintf(fp, "format:\t%s\n", tmap_refseq_get_version_format(refseq->package_version->s));
tmap_file_fprintf(fp, "package version:\t%s\n", refseq->package_version->s);
for(i=0;i<refseq->num_annos;i++) {
tmap_file_fprintf(fp, "contig-%d:\t%s\t%u\n", i+1, refseq->annos[i].name->s, refseq->annos[i].len);
}
tmap_file_fprintf(fp, "length:\t%llu\n", (unsigned long long int)refseq->len);
tmap_file_fprintf(fp, "supported:\t%s\n", (0 == tmap_refseq_supported(refseq)) ? "false" : "true");
}
int
tmap_index(int argc, char *argv[])
{
int c;
tmap_index_opt_t opt;
opt.fn_fasta = NULL;
opt.occ_interval = TMAP_BWT_OCC_INTERVAL;
opt.hash_width = INT32_MAX;
opt.sa_interval = TMAP_SA_INTERVAL;
opt.is_large = -1;
opt.check_hash = 1;
if(2 == argc && 0 == strcmp("--version", argv[1])) {
tmap_file_stdout = tmap_file_fdopen(fileno(stdout), "wb", TMAP_FILE_NO_COMPRESSION);
tmap_file_fprintf(tmap_file_stdout, "%s\n", tmap_refseq_get_version_format(PACKAGE_VERSION));
tmap_file_fclose(tmap_file_stdout);
return 0;
}
while((c = getopt(argc, argv, "f:o:i:w:a:hvH")) >= 0) {
switch(c) {
case 'f':
opt.fn_fasta = tmap_strdup(optarg); break;
case 'o':
opt.occ_interval = atoi(optarg); break;
case 'i':
opt.sa_interval = atoi(optarg); break;
case 'w':
opt.hash_width = atoi(optarg); break;
case 'a':
if(0 == strcmp("is", optarg)) opt.is_large = 0;
else if(0 == strcmp("bwtsw", optarg)) opt.is_large = 1;
else tmap_error("Option -a value not correct", Exit, CommandLineArgument);
break;
case 'v':
tmap_progress_set_verbosity(1); break;
case 'h':
return usage(&opt);
case 'H':
opt.check_hash = 0; break;
default:
return usage(&opt);
}
}
if(argc != optind || 1 == argc) {
return usage(&opt);
}
if(NULL == opt.fn_fasta) {
tmap_error("required option -f", Exit, CommandLineArgument);
}
if(opt.occ_interval < TMAP_BWT_OCC_MOD || 0 != (opt.occ_interval % 2) || 0 != (opt.occ_interval % TMAP_BWT_OCC_MOD)) {
tmap_error("option -o out of range", Exit, CommandLineArgument);
}
if(opt.hash_width < 0) {
tmap_error("option -w out of range", Exit, CommandLineArgument);
}
if(opt.sa_interval <= 0 || (1 < opt.sa_interval && 0 != (opt.sa_interval % 2))) {
tmap_error("option -i out of range", Exit, CommandLineArgument);
}
tmap_index_core(&opt);
free(opt.fn_fasta);
tmap_progress_print2("terminating successfully");
return 0;
}
