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 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;
}