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[])
{
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;
}
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;
}