int main(int argc, char *argv[]) { if (argc < 2) return usage(); if (strcmp(argv[1], "fa2pac") == 0) return bwa_fa2pac(argc-1, argv+1); else if (strcmp(argv[1], "pac2bwt") == 0) return bwa_pac2bwt(argc-1, argv+1); else if (strcmp(argv[1], "pac2bwtgen") == 0) return bwt_bwtgen_main(argc-1, argv+1); else if (strcmp(argv[1], "bwtupdate") == 0) return bwa_bwtupdate(argc-1, argv+1); else if (strcmp(argv[1], "pac_rev") == 0) return bwa_pac_rev(argc-1, argv+1); else if (strcmp(argv[1], "bwt2sa") == 0) return bwa_bwt2sa(argc-1, argv+1); else if (strcmp(argv[1], "index") == 0) return bwa_index(argc-1, argv+1); else if (strcmp(argv[1], "aln") == 0) return bwa_aln(argc-1, argv+1); else if (strcmp(argv[1], "sw") == 0) return bwa_stdsw(argc-1, argv+1); else if (strcmp(argv[1], "samse") == 0) return bwa_sai2sam_se(argc-1, argv+1); else if (strcmp(argv[1], "sampe") == 0) return bwa_sai2sam_pe(argc-1, argv+1); else if (strcmp(argv[1], "pac2cspac") == 0) return bwa_pac2cspac(argc-1, argv+1); else if (strcmp(argv[1], "stdsw") == 0) return bwa_stdsw(argc-1, argv+1); else if (strcmp(argv[1], "bwtsw2") == 0) return bwa_bwtsw2(argc-1, argv+1); else if (strcmp(argv[1], "dbwtsw") == 0) return bwa_bwtsw2(argc-1, argv+1); else if (strcmp(argv[1], "bwasw") == 0) return bwa_bwtsw2(argc-1, argv+1); else { fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); return 1; } return 0; }
int main(int argc, char *argv[]) { struct timeval st; int j; if (argc < 2) return usage(); // ------------------- gettimeofday(&st, NULL); _prog_start = st.tv_sec * 1000000L + (time_t)st.tv_usec; sprintf(bwaversionstr,"%s-%s",mkxstr(PACKAGE_VERS),mkxstr(SVNREV)); sprintf(bwablddatestr,"%s",mkxstr(BLDDATE)); for(j=1;j<argc;j++){ if(strncmp(argv[j],"-ver",4) == 0){ fprintf(stdout,"BWA program (%s)\n", bwaversionstr); return 0; } } // ------------------- if (strcmp(argv[1], "fa2pac") == 0) return bwa_fa2pac(argc-1, argv+1); else if (strcmp(argv[1], "pac2bwt") == 0) return bwa_pac2bwt(argc-1, argv+1); else if (strcmp(argv[1], "pac2bwtgen") == 0) return bwt_bwtgen_main(argc-1, argv+1); else if (strcmp(argv[1], "bwtupdate") == 0) return bwa_bwtupdate(argc-1, argv+1); else if (strcmp(argv[1], "pac_rev") == 0) return bwa_pac_rev(argc-1, argv+1); else if (strcmp(argv[1], "bwt2sa") == 0) return bwa_bwt2sa(argc-1, argv+1); else if (strcmp(argv[1], "index") == 0) return bwa_index(argc-1, argv+1); else if (strcmp(argv[1], "aln") == 0) return bwa_aln(argc-1, argv+1); else if (strcmp(argv[1], "sw") == 0) return bwa_stdsw(argc-1, argv+1); else if (strcmp(argv[1], "samse") == 0) return bwa_sai2sam_se(argc-1, argv+1); else if (strcmp(argv[1], "sampe") == 0) return bwa_sai2sam_pe(argc-1, argv+1); else if (strcmp(argv[1], "pac2cspac") == 0) return bwa_pac2cspac(argc-1, argv+1); else if (strcmp(argv[1], "stdsw") == 0) return bwa_stdsw(argc-1, argv+1); else if (strcmp(argv[1], "bwtsw2") == 0) return bwa_bwtsw2(argc-1, argv+1); else if (strcmp(argv[1], "dbwtsw") == 0) return bwa_bwtsw2(argc-1, argv+1); else if (strcmp(argv[1], "bwasw") == 0) return bwa_bwtsw2(argc-1, argv+1); else { fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); return 1; } return 0; }
int main(int argc, char *argv[]) { int i, ret; double t_real; t_real = realtime(); if (argc < 2) return usage(); if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1); else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1); else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1); else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1); else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1); else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1); else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1); else if (strcmp(argv[1], "sw") == 0) ret = bwa_stdsw(argc-1, argv+1); else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1); else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1); else if (strcmp(argv[1], "pac2cspac") == 0) ret = bwa_pac2cspac(argc-1, argv+1); else if (strcmp(argv[1], "stdsw") == 0) ret = bwa_stdsw(argc-1, argv+1); else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1); else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1); else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1); else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1); else { fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); return 1; } err_fflush(stdout); err_fclose(stdout); if (ret == 0) { fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION); fprintf(stderr, "[%s] CMD:", __func__); for (i = 0; i < argc; ++i) fprintf(stderr, " %s", argv[i]); fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime()); } return 0; }