int main(int argc, char *argv[])
{
void write_sa(char *filename, int *p, int n);
void write_lcp(char *filename, UChar *x,int *p, int n);
void write_bwt(char *filename, UChar *x,int *p, int n);
void check_sa_ordering(UChar *x,int *p, int n, int);
void print_sa_onscreen(UChar *x,int *p, int n, int);
int c, *p, n;
int print_sa, check_sa, num_opt,overshoot;
UChar *x;
clock_t end,start, end_real, start_real;
struct tms r;
double tot_time = 0.0;
double tot_time_real = 0.0;
extern char *optarg;
extern int optind, opterr, optopt;
char *fnam, *sa_filename;
char *lcp_filename,*bwt_filename; // names for (optional) lcp and bwt files
FILE *f;
/* ------------ set default values ------------- */
set_global_variables();
print_sa=check_sa=0;
sa_filename = NULL;
lcp_filename = NULL;
bwt_filename = NULL;
/* ------------- read options from command line ----------- */
num_opt = opterr = 0;
while ((c=getopt(argc, argv, "b:d:l:p:r:w:cvux:f:T:W:B:")) != -1) {
switch (c)
{
case 'b':
bwt_filename = optarg; break;
case 'c':
check_sa++; break;
case 'd':
Anchor_dist = atoi(optarg); break;
case 'l':
Shallow_limit = atoi(optarg); break;
case 'p':
print_sa = atoi(optarg); break;
case 'x':
_ds_Word_size = atoi(optarg); break;
case 'v':
_ds_Verbose++; break;
case 'w':
sa_filename = optarg; break;
case 'f':
Max_pseudo_anchor_offset = atoi(optarg); break;
case 'r':
B2g_ratio = atoi(optarg); break;
case 'u':
Update_anchor_ranks = 1; break;
case 'T':
Mk_qs_thresh = atoi(optarg); break;
case 'W':
lcp_filename = optarg; break;
case 'B':
Blind_sort_ratio = atoi(optarg); break;
case '?':
fprintf(stderr,"Unknown option: %c -main-\n", optopt);
exit(1);
}
num_opt++;
}
if(optind<argc)
fnam=argv[optind];
else {
fprintf(stderr, "Usage:\n\t%s [-b bwtfile][-cuv][-d dist]",argv[0]);
fprintf(stderr, "[-l len][-p num][-f maxoff][-r ratio]\n");
fprintf(stderr,
"\t [-T thresh][-w safile][-W lcpfile][-x wsize][-B ratio]");
fprintf(stderr, " file\n\n");
fprintf(stderr,"\t-b bwtfile write bwt to bwtfile\n");
fprintf(stderr,
"\t-B ratio blind_sort ratio [def. %d]\n",Blind_sort_ratio);
fprintf(stderr,"\t-c check the sa (could be very slow)\n");
fprintf(stderr,"\t-d dist anchor distance [def. %d]\n",Anchor_dist);
fprintf(stderr,"\t-f maxoff Maximum offset for forward ");
fprintf(stderr,"pseudo-anchors [def. %d]\n",Max_pseudo_anchor_offset);
fprintf(stderr,
"\t-l len shallow sort limit [def. %d]\n",Shallow_limit);
fprintf(stderr,
"\t-r ratio bucket to group max ratio [def. %d]\n",B2g_ratio);
fprintf(stderr,"\t-p num print num char of each suffix [def. 0]\n");
fprintf(stderr,
"\t-T thresh Threshold for mk-qs [def. %d]\n", Mk_qs_thresh);
fprintf(stderr,"\t-u updates anchor ranks in get_rank()\n");
fprintf(stderr,"\t-v produces a verbose output\n");
fprintf(stderr,"\t-w safile write sa to safile\n");
fprintf(stderr,
"\t-W lcpfile check sa and write lcp to lcpfile (very slow)\n");
fprintf(stderr,
"\t-x wsize word size in mkqs (default %d)\n\n",_ds_Word_size);
return 0;
}
if(_ds_Verbose) {
fprintf(stderr,"Command line: ");
for(c=0;c<argc;c++)
fprintf(stderr,"%s ",argv[c]);
fprintf(stderr,"\n");
}
/* -------- check parameters ------------- */
if(check_global_variables()) {
exit(1);
}
/* ---------- open file and read text ----------- */
if (! (f=fopen(fnam, "rb"))) {
perror(fnam);
return 1;
}
if (fseek(f, 0L, SEEK_END)) {
perror(fnam);
return 1;
}
n=ftell(f);
if (n==0) {
fprintf(stderr, "%s: file empty\n", fnam);
return 0;
}
// ------ allocate memory for text and sa -------
overshoot = compute_overshoot();
p=malloc((n)*sizeof *p); // sa
x=malloc((n+overshoot)*sizeof *x); // text
if (! p || ! x) {
fprintf(stderr, "malloc failed\n");
return 1;
}
// ------------ read input text ---------------
rewind(f);
c=fread(x, (size_t) 1, (size_t) n, f);
// lseek(fileno(f),0,SEEK_SET);
// c=read(fileno(f), x, (size_t) n);
if(c!=n) {
fprintf(stderr,"Error in read() (%d vs %d) (main)\n",c,n);
perror(fnam);
return 1;
}
fclose(f);
/* --------- start measuring time ------------- */
if(_ds_Verbose)
fprintf(stderr,"Starting sa construction ... \n");
start_real = times(&r);
start = (r.tms_utime+r.tms_stime); /* user + system */
ds_ssort(x, p, n);
end_real = times(&r);
end = (r.tms_utime+r.tms_stime); /* user + system */
// tot_time = ((double) (end-start))/CLK_TCK;
//tot_time_real = ((double) (end_real-start_real))/CLK_TCK;
printf("Elapsed time: %.2f seconds (user+sys). Total real time: %.2f.\n",
tot_time, tot_time_real);
// --------------- write bwt to a file
if(bwt_filename!=NULL)
write_bwt(bwt_filename,x,p,n);
// --------------- write sa to a file
if(sa_filename!=NULL)
write_sa(sa_filename,p,n);
// --------------- write lcp to a file
if(lcp_filename!=NULL)
write_lcp(lcp_filename,x,p,n);
// ------------ check sa --------
if(check_sa)
check_sa_ordering(x,p,n,check_sa);
// ----- display sa -------
if(print_sa)
print_sa_onscreen(x,p,n,print_sa);
// deallocate and exit
free(x); free(p);
return 0;
}
void csa_new_from_bwt(CSA csa, char *fname, char *fidx, int psi_id, int idx_id, bool coded)
{
int k;
i64 i,j,v,m;
FILE *f2;
i64 psize,isize;
i64 n;
psi_id = csa.id;
if (psi_id >= 0) {
printf("create psi: id=%d\n",psi_id);
}
if (idx_id >= 0) {
printf("create idx: id=%d D=%d D2=%d\n",idx_id,csa.D,csa.D2);
}
psize = 0;
if (psi_id >= 0) {
switch (psi_id & 0x3f) {
case ID_DIFF_GAMMA:
case ID_DIFF_GAMMA_RL:
case ID_DIFF_GAMMA_SPARSE:
case ID_DIFF_GAMMA_RL_SPARSE:
psize = psi1_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_DIFF_GAMMA_RR:
psize = psi12_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_DNA:
psize = lf_dna_makeindex(&csa, fname, coded);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_BIT:
psize = lf_bit_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_WT:
case ID_BWT_WT_HUF:
case ID_BWT_WT_DENSE:
case ID_BWT_WT_SPARSE4:
case ID_BWT_WT_RR:
psize = lf_wt_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
#if 0
case ID_BWT_HUF:
psize = lf_bwt_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
#endif
case ID_SPARSE4:
psize = psi2_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
default:
printf("psi_id = %d\n",psi_id);
exit(1);
}
}
csa.k = (blog(csa.n+1)+1+8-1)/8;
for (i=0; i<SIGMA; i++) csa.CtoA[i] = -1;
// csa.K[-1+1] = 0;
csa.K[-1+1] = 1;
for (m=0,v=1,i=0; i<SIGMA; i++) {
if (csa.C[i]>0) {
csa.AtoC[m] = i;
csa.CtoA[i] = m;
csa.K[m+1] = v;
// printf("i=%ld v = %ld C[i] = %ld\n",i,v,csa.C[i]);
v += csa.C[i];
m++;
}
}
csa.K[m+1] = v;
csa.m = m;
if (csa.D >= csa.n) {
printf("D=%d >= n=%ld\n",csa.D,csa.n);
exit(0);
}
if (csa.D2 >= csa.n) {
printf("D2=%d >= n=%ld\n",csa.D2,csa.n);
exit(0);
}
if (idx_id >= 0) {
n = csa.n;
k = csa.k;
//// compute SA and ISA
if (csa.D > 0) csa.SA = (uchar *) mymalloc(((n-1)/csa.D+1+1)*k);
if (csa.D2 > 0) csa.ISA = (uchar *) mymalloc(((n-1)/csa.D2+1+1)*k);
if (csa.D == 0 && csa.D2 == 0) goto brk;
switch (psi_id & 0x3f) {
case ID_DIFF_GAMMA:
case ID_DIFF_GAMMA_RL:
case ID_DIFF_GAMMA_SPARSE:
case ID_DIFF_GAMMA_RL_SPARSE:
case ID_SPARSE4:
case ID_DIFF_GAMMA_RR:
j = 0;
for (i=0; i<=n; i++) {
display_progressbar("making sa ",i,n);
j = csa.psi(&csa,j);
// sa[j] = i;
if (csa.D > 0 && j % csa.D == 0) {
putuint(csa.SA,j / csa.D,i,k);
}
if (csa.D2 > 0 && i % csa.D2 == 0) {
putuint(csa.ISA,i / csa.D2,j,k);
}
}
// putuint(csa.SA,0,n,k);
break;
case ID_BWT_DNA:
case ID_BWT_BIT:
case ID_BWT_WT:
case ID_BWT_WT_HUF:
case ID_BWT_WT_DENSE:
case ID_BWT_WT_SPARSE4:
case ID_BWT_WT_RR:
case ID_BWT_HUF:
j = 0;
for (i=n-1; i>=0; i--) {
display_progressbar("making sa ",i,n);
v = csa.LF(&csa,j);
// printf("LF[%ld] = %ld\n",j,v);
j = v;
if (csa.D > 0 && j % csa.D == 0) putuint(csa.SA, j/csa.D , i, k);
if (csa.D2 > 0 && i % csa.D2 == 0) putuint(csa.ISA, i/csa.D2, j, k);
}
putuint(csa.SA,0,n,k);
break;
default:
break;
}
brk:
//// write idx
f2 = fopen(fidx,"wb"); /* directory */
if (f2 == NULL) {
perror("csa2_new1: ");
exit(1);
}
isize = 0;
writeint(4,VERSION,f2); /* version */
isize += 4;
writeint(1,ID_HEADER,f2); // header ID
isize += 1;
isize = write_header(&csa, f2, isize);
if (csa.D > 0) {
writeint(1,ID_SA,f2);
isize += 1;
isize = write_sa(&csa, f2, isize);
}
if (csa.D2 > 0) {
writeint(1,ID_ISA,f2);
isize += 1;
isize = write_isa(&csa, f2, isize);
}
fclose(f2);
if (csa.D > 0) free(csa.SA);
if (csa.D2 > 0) free(csa.ISA);
printf("Total %ld bytes (%1.3f bpc)\n",(psize+isize),
(double)(psize+isize)*8/csa.n);
}
free(fidx);
}
void csa_new_from_bwt(int argc, char *argv[])
{
i64 i,j,v,m;
FILE *f2;
i64 psize,isize;
i64 n;
int k;
char *fname,*fidx;
char *p;
int psi_id, idx_id;
CSA csa;
int sigma;
csa.sigma = 256; /* default alphabet size */
csa.k2 = 1;
// for (i=0; i<SIGMA+2; i++) csa.C[i] = 0;
// for (i=0; i<SIGMA; i++) csa.C[i] = 0;
fname = NULL; fidx = NULL;
psi_id = idx_id = -1;
for (i=1; i<argc; i++) {
p = argv[i];
if (p[0] == '-') {
p++;
switch (toupper(p[0])) {
case 'I':
// -I[n]:[D]:[D2]
p++;
idx_id = 0;
csa_options(&csa, p);
break;
case 'P':
// -P[n]:[L]
p++;
psi_id = 0;
psi_options(&csa, p);
break;
case 'C':
// -C[s]
p++;
sigma_options(&csa, p);
break;
default:
printf("??? no such option %s\n",argv[i]);
exit(1);
}
} else {
fname = argv[i];
k = strlen(fname);
fidx = mymalloc(k+5);
sprintf(fidx,"%s.idx",fname);
}
}
if (fname == NULL) {
printf("no input file.\n");
exit(0);
}
printf("sigma = %d k2 = %d\n", csa.sigma, csa.k2);
sigma = csa.sigma;
csa.C = mymalloc(sizeof(*csa.C)*sigma); //
csa.CtoA = mymalloc(sizeof(*csa.CtoA)*sigma); //
csa.AtoC = mymalloc(sizeof(*csa.AtoC)*sigma); //
csa.K = mymalloc(sizeof(*csa.K)*(sigma+2)); //
for (i=0; i<sigma; i++) csa.C[i] = 0;
psi_id = csa.id;
if (psi_id >= 0) {
printf("create psi: id=%d\n",psi_id);
}
if (idx_id >= 0) {
printf("create idx: id=%d D=%d D2=%d\n",idx_id,csa.D,csa.D2);
}
psize = 0;
if (psi_id >= 0) {
switch (psi_id & 0x3f) {
case ID_DIFF_GAMMA:
case ID_DIFF_GAMMA_RL:
case ID_DIFF_GAMMA_SPARSE:
case ID_DIFF_GAMMA_RL_SPARSE:
psize = psi1_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_DIFF_GAMMA_RR:
psize = psi12_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_DNA:
psize = lf_dna_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_DNA2:
psize = lf_dna2_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_BIT:
psize = lf_bit_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_WT:
case ID_BWT_WT_HUF:
case ID_BWT_WT_DENSE:
case ID_BWT_WT_SPARSE4:
case ID_BWT_WT_RR:
psize = lf_wt_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
#if 0
case ID_BWT_HUF:
psize = lf_bwt_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
#endif
case ID_SPARSE4:
psize = psi2_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
default:
printf("psi_id = %d\n",psi_id);
exit(1);
}
}
csa.k = (blog(csa.n+1)+1+8-1)/8;
for (i=0; i<sigma; i++) csa.CtoA[i] = -1;
csa.K[-1+1] = 1;
for (m=0,v=1,i=0; i<sigma; i++) {
if (csa.C[i]>0) {
csa.AtoC[m] = i;
csa.CtoA[i] = m;
csa.K[m+1] = v;
// printf("i=%ld v = %ld C[i] = %ld\n",i,v,csa.C[i]);
v += csa.C[i];
m++;
}
}
csa.K[m+1] = v;
csa.m = m;
if (csa.D >= csa.n) {
printf("D=%d >= n=%ld\n",csa.D,csa.n);
exit(0);
}
if (csa.D2 >= csa.n) {
printf("D2=%d >= n=%ld\n",csa.D2,csa.n);
exit(0);
}
if (idx_id >= 0) {
n = csa.n;
k = csa.k;
//// compute SA and ISA
if (csa.D > 0) csa.SA = mymalloc(((n-1)/csa.D+1+1)*k);
if (csa.D2 > 0) csa.ISA = mymalloc(((n-1)/csa.D2+1+1)*k);
if (csa.D == 0 && csa.D2 == 0) goto brk;
switch (psi_id & 0x3f) {
case ID_DIFF_GAMMA:
case ID_DIFF_GAMMA_RL:
case ID_DIFF_GAMMA_SPARSE:
case ID_DIFF_GAMMA_RL_SPARSE:
case ID_SPARSE4:
case ID_DIFF_GAMMA_RR:
j = 0;
for (i=0; i<=n; i++) {
display_progressbar("making sa ",i,n);
j = csa.psi(&csa,j);
// sa[j] = i;
if (csa.D > 0 && j % csa.D == 0) {
putuint(csa.SA,j / csa.D,i,k);
}
if (csa.D2 > 0 && i % csa.D2 == 0) {
putuint(csa.ISA,i / csa.D2,j,k);
}
}
// putuint(csa.SA,0,n,k);
break;
case ID_BWT_DNA:
case ID_BWT_DNA2:
case ID_BWT_BIT:
case ID_BWT_WT:
case ID_BWT_WT_HUF:
case ID_BWT_WT_DENSE:
case ID_BWT_WT_SPARSE4:
case ID_BWT_WT_RR:
case ID_BWT_HUF:
j = 0;
for (i=n-1; i>=0; i--) {
display_progressbar("making sa ",i,n);
v = csa.LF(&csa,j);
// printf("LF[%ld] = %ld\n",j,v);
j = v;
if (csa.D > 0 && j % csa.D == 0) putuint(csa.SA, j/csa.D , i, k);
if (csa.D2 > 0 && i % csa.D2 == 0) putuint(csa.ISA, i/csa.D2, j, k);
}
// putuint(csa.SA,0,n,k);
if (csa.D > 0) putuint(csa.SA,0,n,k); // 2011-12-20
break;
default:
break;
}
brk:
//// write idx
f2 = fopen(fidx,"wb"); /* directory */
if (f2 == NULL) {
perror("csa2_new1: ");
exit(1);
}
isize = 0;
writeint(4,VERSION,f2); /* version */
isize += 4;
writeint(1,ID_HEADER,f2); // header ID
isize += 1;
isize = write_header(&csa, f2, isize);
if (csa.D > 0) {
writeint(1,ID_SA,f2);
isize += 1;
isize = write_sa(&csa, f2, isize);
}
if (csa.D2 > 0) {
writeint(1,ID_ISA,f2);
isize += 1;
isize = write_isa(&csa, f2, isize);
}
fclose(f2);
if (csa.D > 0) free(csa.SA);
if (csa.D2 > 0) free(csa.ISA);
printf("Total %ld bytes (%1.3f bpc)\n",(psize+isize),
(double)(psize+isize)*8/csa.n);
}
free(fidx);
}
