int
main(int argc, char *argv[])
{
int ret = 0;
tmap_command_t *c = NULL;
if(argc < 2) {
return tmap_usage(argc, argv);
}
else {
tmap_file_stderr = tmap_file_fdopen(fileno(stderr), "w", TMAP_FILE_NO_COMPRESSION); // set stderr
tmap_progress_set_command(argv[1]); // set output progress
tmap_progress_set_start_time(); // set start time
bam_verbose = 0; // No verbosity in SAMtools
c = commands;
while(0 <= c->type) {
if (0 == strcmp(c->name, argv[1])) {
ret = c->func(argc-1, argv+1);
break;
}
c++;
}
if(c->type < 0) {
tmap_help_unknown_cmd(argv[1]);
tmap_error1(PACKAGE, "Unknown command", Exit, CommandLineArgument);
}
// NB: do not close the underlying stderr stream!
tmap_file_fclose1(tmap_file_stderr, 0);
}
return ret;
}
int
tmap_refseq_refinfo_main(int argc, char *argv[])
{
int c, help=0;
tmap_refseq_t *refseq = NULL;
tmap_file_t *fp_anno = NULL;
char *fn_anno = NULL;
char *fn_fasta = NULL;
while((c = getopt(argc, argv, "vh")) >= 0) {
switch(c) {
case 'v': tmap_progress_set_verbosity(1); break;
case 'h': help = 1; break;
default: return 1;
}
}
if(1 != argc - optind || 1 == help) {
tmap_file_fprintf(tmap_file_stderr, "Usage: %s %s [-vh] <in.fasta>\n", PACKAGE, argv[0]);
return 1;
}
fn_fasta = argv[optind];
// Note: 'tmap_file_stdout' should not have been previously modified
tmap_file_stdout = tmap_file_fdopen(fileno(stdout), "wb", TMAP_FILE_NO_COMPRESSION);
// allocate some memory
refseq = tmap_calloc(1, sizeof(tmap_refseq_t), "refseq");
refseq->is_rev = 0;
refseq->is_shm = 0;
// read the annotation file
fn_anno = tmap_get_file_name(fn_fasta, TMAP_ANNO_FILE);
fp_anno = tmap_file_fopen(fn_anno, "rb", TMAP_ANNO_COMPRESSION);
tmap_refseq_read_anno(fp_anno, refseq);
tmap_file_fclose(fp_anno);
free(fn_anno);
// no need to read in the pac
refseq->seq = NULL;
// print the header
tmap_refseq_print_header(tmap_file_stdout, refseq);
// destroy
tmap_refseq_destroy(refseq);
// close the output
tmap_file_fclose(tmap_file_stdout);
return 0;
}
int main(int argc, char *argv[])
{
int ret = 0;
if(argc < 2) {
return usage();
}
else {
tmap_file_stderr = tmap_file_fdopen(fileno(stderr), "w", TMAP_FILE_NO_COMPRESSION); // set stderr
tmap_progress_set_command(argv[1]); // set output progress
tmap_progress_set_start_time(); // set start time
if (0 == strcmp("index", argv[1])) ret = tmap_index(argc-1, argv+1);
else if (0 == strcmp("server", argv[1])) ret = tmap_server_main(argc-1, argv+1);
else if (0 == strcmp("map1", argv[1])) ret = tmap_map1_main(argc-1, argv+1);
else if (0 == strcmp("map2", argv[1])) ret = tmap_map2_main(argc-1, argv+1);
else if (0 == strcmp("map3", argv[1])) ret = tmap_map3_main(argc-1, argv+1);
else if (0 == strcmp("mapvsw", argv[1])) ret = tmap_map_vsw_main(argc-1, argv+1);
else if (0 == strcmp("mapall", argv[1])) ret = tmap_map_all_main(argc-1, argv+1);
else if (0 == strcmp("fasta2pac", argv[1])) ret = tmap_refseq_fasta2pac_main(argc-1, argv+1);
else if (0 == strcmp("pac2bwt", argv[1])) ret = tmap_bwt_pac2bwt_main(argc-1, argv+1);
else if (0 == strcmp("bwt2sa", argv[1])) ret = tmap_sa_bwt2sa_main(argc-1, argv+1);
else if (0 == strcmp("sff2fq", argv[1])) ret = tmap_seq_io_sff2fq_main(argc-1, argv+1);
else if (0 == strcmp("refinfo", argv[1])) ret = tmap_refseq_refinfo_main(argc-1, argv+1);
else if (0 == strcmp("pac2fasta", argv[1])) ret = tmap_refseq_pac2fasta_main(argc-1, argv+1);
#ifdef HAVE_SAMTOOLS
else if (0 == strcmp("sam2fs", argv[1])) ret = tmap_sam2fs_main(argc-1, argv+1);
#endif
#ifdef ENABLE_TMAP_DEBUG_FUNCTIONS
else if (0 == strcmp("exact", argv[1])) ret = tmap_debug_exact(argc-1, argv+1);
else if (0 == strcmp("fsw", argv[1])) ret = tmap_fsw_main(argc-1, argv+1);
else if (0 == strcmp("indexspeed", argv[1])) ret = tmap_index_speed(argc-1, argv+1);
else if (0 == strcmp("vswbm", argv[1])) ret = tmap_vswbm_main(argc-1, argv+1);
#endif
else if (0 == strcmp("--version", argv[1]) || 0 == strcmp("-v", argv[1])) ret = version();
else if (0 == strcmp("--help", argv[1]) || 0 == strcmp("-h", argv[1])) ret = usage();
else {
tmap_error1(PACKAGE, "Unknown command", Exit, CommandLineArgument);
}
// NB: do not close the underlying stderr stream!
tmap_file_fclose1(tmap_file_stderr, 0);
}
return ret;
}
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;
}
int
tmap_refseq_pac2fasta_main(int argc, char *argv[])
{
int c, help=0, amb=0;
uint32_t i, j, k;
char *fn_fasta = NULL;
tmap_refseq_t *refseq = NULL;
while((c = getopt(argc, argv, "avh")) >= 0) {
switch(c) {
case 'a': amb = 1; break;
case 'v': tmap_progress_set_verbosity(1); break;
case 'h': help = 1; break;
default: return 1;
}
}
if(1 != argc - optind || 1 == help) {
tmap_file_fprintf(tmap_file_stderr, "Usage: %s %s [-avh] <in.fasta>\n", PACKAGE, argv[0]);
return 1;
}
fn_fasta = argv[optind];
// Note: 'tmap_file_stdout' should not have been previously modified
tmap_file_stdout = tmap_file_fdopen(fileno(stdout), "wb", TMAP_FILE_NO_COMPRESSION);
// read in the reference sequence
refseq = tmap_refseq_read(fn_fasta, 0);
for(i=0;i<refseq->num_annos;i++) {
tmap_file_fprintf(tmap_file_stdout, ">%s", refseq->annos[i].name->s); // new line handled later
for(j=k=0;j<refseq->annos[i].len;j++) {
if(0 == (j % TMAP_REFSEQ_FASTA_LINE_LENGTH)) {
tmap_file_fprintf(tmap_file_stdout, "\n");
}
if(1 == amb && 0 < refseq->annos[i].num_amb) {
// move the next ambiguous region
while(k < refseq->annos[i].num_amb && refseq->annos[i].amb_positions_end[k] < j+1) {
k++;
}
// check for the ambiguous region
if(k < refseq->annos[i].num_amb
&& 0 == tmap_interval_overlap(j+1, j+1, refseq->annos[i].amb_positions_start[k], refseq->annos[i].amb_positions_end[k])) {
tmap_file_fprintf(tmap_file_stdout, "%c", tmap_iupac_int_to_char[refseq->annos[i].amb_bases[k]]);
}
else {
tmap_file_fprintf(tmap_file_stdout, "%c", "ACGTN"[(int)tmap_refseq_seq_i(refseq, j + refseq->annos[i].offset)]);
}
}
else {
tmap_file_fprintf(tmap_file_stdout, "%c", "ACGTN"[(int)tmap_refseq_seq_i(refseq, j + refseq->annos[i].offset)]);
}
}
tmap_file_fprintf(tmap_file_stdout, "\n");
}
// destroy
tmap_refseq_destroy(refseq);
// close the output
tmap_file_fclose(tmap_file_stdout);
return 0;
}