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;
}
int bwa_index(int argc, char *argv[])
{
char *prefix = 0, *str, *str2, *str3;
int c, algo_type = 0, is_color = 0, is_64 = 0;
clock_t t;
int64_t l_pac;
while ((c = getopt(argc, argv, "6ca:p:")) >= 0) {
switch (c) {
case 'a': // if -a is not set, algo_type will be determined later
if (strcmp(optarg, "div") == 0) algo_type = 1;
else if (strcmp(optarg, "bwtsw") == 0) algo_type = 2;
else if (strcmp(optarg, "is") == 0) algo_type = 3;
else err_fatal(__func__, "unknown algorithm: '%s'.", optarg);
break;
case 'p': prefix = strdup(optarg); break;
case 'c': is_color = 1; break;
case '6': is_64 = 1; break;
default: return 1;
}
}
if (optind + 1 > argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bwa index [-a bwtsw|is] [-c] <in.fasta>\n\n");
fprintf(stderr, "Options: -a STR BWT construction algorithm: bwtsw or is [auto]\n");
fprintf(stderr, " -p STR prefix of the index [same as fasta name]\n");
fprintf(stderr, " -6 index files named as <in.fasta>.64.* instead of <in.fasta>.* \n");
// fprintf(stderr, " -c build color-space index\n");
fprintf(stderr, "\n");
fprintf(stderr, "Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n");
fprintf(stderr, " `-a div' do not work not for long genomes. Please choose `-a'\n");
fprintf(stderr, " according to the length of the genome.\n\n");
return 1;
}
if (prefix == 0) {
prefix = malloc(strlen(argv[optind]) + 4);
strcpy(prefix, argv[optind]);
if (is_64) strcat(prefix, ".64");
}
str = (char*)calloc(strlen(prefix) + 10, 1);
str2 = (char*)calloc(strlen(prefix) + 10, 1);
str3 = (char*)calloc(strlen(prefix) + 10, 1);
if (is_color == 0) { // nucleotide indexing
gzFile fp = xzopen(argv[optind], "r");
t = clock();
fprintf(stderr, "[bwa_index] Pack FASTA... ");
l_pac = bns_fasta2bntseq(fp, prefix, 0);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
gzclose(fp);
} else { // color indexing
gzFile fp = xzopen(argv[optind], "r");
strcat(strcpy(str, prefix), ".nt");
t = clock();
fprintf(stderr, "[bwa_index] Pack nucleotide FASTA... ");
l_pac = bns_fasta2bntseq(fp, str, 0);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
gzclose(fp);
{
char *tmp_argv[3];
tmp_argv[0] = argv[0]; tmp_argv[1] = str; tmp_argv[2] = prefix;
t = clock();
fprintf(stderr, "[bwa_index] Convert nucleotide PAC to color PAC... ");
bwa_pac2cspac(3, tmp_argv);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
}
}
if (algo_type == 0) algo_type = l_pac > 50000000? 2 : 3; // set the algorithm for generating BWT
{
strcpy(str, prefix); strcat(str, ".pac");
strcpy(str2, prefix); strcat(str2, ".bwt");
t = clock();
fprintf(stderr, "[bwa_index] Construct BWT for the packed sequence...\n");
if (algo_type == 2) bwt_bwtgen(str, str2);
else if (algo_type == 1 || algo_type == 3) {
bwt_t *bwt;
bwt = bwt_pac2bwt(str, algo_type == 3);
bwt_dump_bwt(str2, bwt);
bwt_destroy(bwt);
}
fprintf(stderr, "[bwa_index] %.2f seconds elapse.\n", (float)(clock() - t) / CLOCKS_PER_SEC);
}
{
bwt_t *bwt;
strcpy(str, prefix); strcat(str, ".bwt");
t = clock();
fprintf(stderr, "[bwa_index] Update BWT... ");
bwt = bwt_restore_bwt(str);
bwt_bwtupdate_core(bwt);
bwt_dump_bwt(str, bwt);
bwt_destroy(bwt);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
}
{
gzFile fp = xzopen(argv[optind], "r");
t = clock();
fprintf(stderr, "[bwa_index] Pack forward-only FASTA... ");
l_pac = bns_fasta2bntseq(fp, prefix, 1);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
gzclose(fp);
}
{
bwt_t *bwt;
strcpy(str, prefix); strcat(str, ".bwt");
strcpy(str3, prefix); strcat(str3, ".sa");
t = clock();
fprintf(stderr, "[bwa_index] Construct SA from BWT and Occ... ");
bwt = bwt_restore_bwt(str);
bwt_cal_sa(bwt, 32);
bwt_dump_sa(str3, bwt);
bwt_destroy(bwt);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
}
free(str3); free(str2); free(str); free(prefix);
return 0;
}
