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; }