C++ (Cpp) bwa_bwtupdateの例

プログラミング言語: C++ (Cpp)

メソッド/関数: bwa_bwtupdate

hotexamples.comのコード掲載数: 4

C++ (Cpp) bwa_bwtupdate - 4件のコード例が見つかりました。すべてオープンソースプロジェクトから抽出されたC++ (Cpp)のbwa_bwtupdateの実例で、最も評価が高いものを厳選しています。コード例の評価を行っていただくことで、より質の高いコード例が表示されるようになります。

コード例 #1

ファイルを表示

ファイル: main.c プロジェクト: 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;
}

コード例 #2

ファイルを表示

ファイル: main.c プロジェクト: jwbargsten/bwa

int main(int argc, char *argv[])
{
	int i, ret;
	double t_real;
	kstring_t pg = {0,0,0};
	t_real = realtime();
	ksprintf(&pg, "@PG\tID:bwa\tPN:bwa\tVN:%s\tCL:%s", PACKAGE_VERSION, argv[0]);
	for (i = 1; i < argc; ++i) ksprintf(&pg, " %s", argv[i]);
	bwa_pg = pg.s;
	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], "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], "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 if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
	else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
	else {
		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
		return 1;
	}
#ifdef USE_HTSLIB
	if (strcmp(argv[1], "mem") != 0) { 
		err_fflush(stdout);
		err_fclose(stdout);
	}
#else
	err_fflush(stdout);
	err_fclose(stdout);
#endif
	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());
	}
	free(bwa_pg);
	return ret;
}

コード例 #3

ファイルを表示

ファイル: main.c プロジェクト: 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;
}

コード例 #4

ファイルを表示

ファイル: main.c プロジェクト: RoelKluin/bwa

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;
}