C++ (Cpp) bwa_pac_rev Examples

Example #1

File: main.c Project: fstrozzi/bioruby-bwa

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;
}

Example #2

File: main.c Project: chumingc/BigBWA

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;
}