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main.c
1010 lines (887 loc) · 30 KB
/
main.c
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// vim: noai:ts=2:sw=2
/*
* gsufsort
*
* Authors: Felipe A. Louza
* contact: louza@usp.br
* 18/09/2018
*
*/
#include <stdio.h>
#include <errno.h>
#include <time.h>
#include <limits.h>
#include <assert.h>
#include <getopt.h>
#include "lib/utils.h"
#include "lib/file.h"
#include "external/gsacak.h"
#include "lib/rankbv.h"
#define SIGMA 256
#ifndef DEBUG
#define DEBUG 0
#endif
#define WORD (size_t)(pow(256,sizeof(int_t))/2.0)
int store_to_disk(unsigned char *T, int_da *DA, rankbv_t* rbv, int_t *SA, int_t *LCP, size_t n, char* c_file, char *ext, int wsize1, int wsize2, int wsize3);
size_t load_from_disk(unsigned char **T, int_da **DA, int_t **SA, int_t **LCP, char* c_file, char *ext, int wsize1, int wsize2, int wsize3);
/******************************************************************************/
void usage(char *name){
printf("\n\tUsage: %s FILENAME [options]\n\n",name);
puts("Extensions supported: txt (raw files) fasta and fastq");
puts("Available options:");
puts("\t--build (default)");
puts("\t--load load from disk FILENAME[.sa][.da][.lcp][.gsa][.str]");
puts("\t--sa [w] compute SA (default) using w (def 4) bytes (FILENAME.w.sa)");
puts("\t--isa [w] compute ISA (FILENAME.w.isa)");
puts("\t--lcp [w] compute LCP (FILENAME.w.lcp)");
puts("\t--da [w] compute DA (FILENAME.w.da)");
puts("\t--gsa [w1][w2] compute GSA=(text, suff) using pairs of (w1, w2) bytes (FILENAME.w1.w2.gsa)");
puts("\t--light run lightweight algorithm to compute DA (also GSA)");
puts("\t--gesa [w1][w2][w3] compute GESA=(GSA.text, GSA.suff, LCP, BWT) (FILENAME.w1.w2.w3.1.gesa)");
puts("\t--bwt compute BWT using 1 byte per symbol (FILENAME.bwt)");
puts("\t--ibwt invert the BWT, given FILENAME[.bwt]");
puts("\t--qs output (only for fastq) QS permuted according to the BWT (FILENAME.bwt.qs)");
puts("\t--str output concatenated input T^{cat} (FILENAME.1.str)");
puts("\t--docs d number of strings (def all FILENAME)");
puts("\t--print p print arrays (stdout) A[1,p]");
puts("\t--lcp_max output maximum LCP (FILENAME.lcp_max)");
puts("\t--lcp_max_text output maximum LCP in text (FILENAME.lcp_max.txt)");
puts("\t--lcp_avg output average LCP (FILENAME.lcp_avg)");
puts("\t--trlcp k output k-truncated LCP array (FILENAME.w.lcp)");
puts("\t--lower convert input symbols to lowercase");
puts("\t--upper convert input symbols to uppercase");
puts("\t--time output time (seconds)");
puts("\t--txt handle input (FILENAME) as raw file (one string per line)");
puts("\t--fasta handle input (FILENAME) as FASTA");
puts("\t--fastq handle input (FILENAME) as FASTQ");
puts("\t--dir handle multiple files in directory (DIR) as input");
puts("\t--output outfile rename output file");
puts("\t--verbose verbose output");
puts("\t--help this help message");
exit(EXIT_FAILURE);
}
/******************************************************************************/
int build=1;
int load=0;
int ibwt=0;
int light=0;
int main(int argc, char** argv){
time_t t_total=0;clock_t c_total=0;
time_t t_start=0;clock_t c_start=0;
int_t i;
int sa=0, isa=0, lcp=0, da=0, bwt=0, q=0, str=0, gsa=0, gesa=0, lcp_max=0, lcp_max_text=0, lcp_avg=0, trlcp=0, time=0, upper=0;
int dir=0;
int in_type=0;// (txt, 1), (fasta, 2) and (fastq, 3)
int sa_bytes=sizeof(int_t);
int isa_bytes=sizeof(int_t);
int lcp_bytes=sizeof(int_t);
int da_bytes=sizeof(int_t);
int t_bytes=sizeof(int_t), s_bytes=sizeof(int_t);
extern char *optarg;
extern int optind;
int c;
char *c_input=NULL, *c_output=NULL;
int d=0; //number of string
int p=0; //print A[1,p]
int output=0; //output
int verbose=0, print=0;
/********/
//int digit_optind = 0;
while (1) {
//int this_option_optind = optind ? optind : 1;
int option_index = 0;
static struct option long_options[] = {
{"print", optional_argument, 0, 'P'},
{"sa", optional_argument, 0, 'S'},
{"isa", optional_argument, 0, 'I'},
{"lcp", optional_argument, 0, 'L'},
{"da", optional_argument, 0, 'D'},
{"gsa", optional_argument, 0, 'g'},
{"bwt", no_argument, 0, 'B'},
{"qs", no_argument, 0, 'Q'},
{"str", no_argument, 0, 'b'},
{"dir", no_argument, 0, 'm'},
{"docs", required_argument, 0, 'd'},
{"verbose", no_argument, 0, 'v'},
{"time", no_argument, 0, 'T'},
{"lower", no_argument, 0, 'u'},
{"upper", no_argument, 0, 'U'},
{"help", no_argument, 0, 'h'},
{"output", required_argument, 0, 'o'},
{"txt", no_argument, 0, 't'},
{"fasta", no_argument, 0, 'f'},
{"fastq", no_argument, 0, 'q'},
{"build", no_argument, 0, '1'},
{"load", no_argument, 0, '2'},
{"ibwt", no_argument, 0, '3'},
{"light", no_argument, 0, 'l'},
{"gesa", optional_argument, 0, 'G'},
{"lcp_max", optional_argument, 0, 'M'},
{"lcp_max_text", optional_argument, 0, 'W'},
{"lcp_avg", optional_argument, 0, 'A'},
{"trlcp", required_argument, 0, 'c'},
{0, 0, 0, 0 }
};
c = getopt_long(argc, argv, "S:vtP:d:L:D:g:lG:B:bhtfqo:ic:Qum", long_options, &option_index);
if (c == -1) break;
switch (c) {
case 0:
printf("option %s", long_options[option_index].name);
if (optarg) printf(" with arg %s", optarg);
printf("\n");
break;
case '1':
build=1; break;
case '2':
load=1; build=0; break;
case '3':
load=0; build=0; ibwt=1; break;
case 'v':
verbose++; break;
case 'l':
light++; break;
case 'T':
time++; break;
case 'P':
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') p = (int) atoi(argv[optind++]);
print=1; break;
case 'S':
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') sa_bytes = (int) atoi(argv[optind++]);
sa=1; break;
case 'I':
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') isa_bytes = (int) atoi(argv[optind++]);
isa=1; break;
case 'L':
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') lcp_bytes = (int) atoi(argv[optind++]);
lcp=1; break;
case 'D':
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') da_bytes = (int) atoi(argv[optind++]);
da=1; break;
case 'g':
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') t_bytes = (int) atoi(argv[optind++]);
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') s_bytes = (int) atoi(argv[optind++]);
gsa=1; break;
case 'B':
bwt=1; break;
case 'Q':
q=1; break;
case 'b':
str=1; break;
case 'G':
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') t_bytes = (int) atoi(argv[optind++]);
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') s_bytes = (int) atoi(argv[optind++]);
if (!optarg && argv[optind] != NULL && argv[optind][0] != '-') lcp_bytes = (int) atoi(argv[optind++]);
gesa=1; break;
case 'd':
d = (int) atoi(optarg); break;
case 'M':
lcp_max=1; break;
case 'W':
lcp_max_text=1; break;
case 'A':
lcp_avg=1; break;
case 'c':
trlcp = (int) atoi(optarg);
lcp=1; break;
case 'u':
upper=1; break; //lowercase
case 'U':
upper=2; break; //uppercase
case 't':
in_type=1; break; //txt
case 'f':
in_type=2; break; //fasta
case 'q':
in_type=3; break; //fastq
case 'm':
dir=1; break; //multiple files in directory FILENAME
case 'h':
usage(argv[0]); break;
case 'o':
c_output=optarg; output=1; break;
case '?':
exit(EXIT_FAILURE);
}
}
/********/
if(optind+1==argc) {
c_input=argv[optind++];
}
else usage(argv[0]);
if(time){
time_start(&t_total, &c_total);
}
if(lcp_max || lcp_avg || lcp_max_text) lcp=1;
if(!bwt && !str && !sa && !isa && !lcp && !da && !gsa && !bwt && !gesa && !ibwt){
//die("choose at least one option [--sa] [--lcp] [--da] [--gsa] [--gesa] [--bwt] [--str]");
sa=1;//default
}
if(!output){
c_output = (char*) malloc(strlen(c_input)+5);
if(dir)
sprintf(c_output, "all");
else
sprintf(c_output, "%s", filename_without_path(c_input));
}
else{
if(c_output[strlen(c_output)-1]=='/'){
char* c_tmp = (char*) malloc(strlen(c_output)+strlen(c_input)+1);
if(dir){
mkdir(c_output);
sprintf(c_tmp, "%s%s", c_output, "all");
}
else
sprintf(c_tmp, "%s%s", c_output, filename_without_path(c_input));
c_output = c_tmp;
output=0;
}
}
if(build){
unsigned char **R;
size_t n=0;
//disk access
if(dir){
R = (unsigned char**) file_load_multiple_dir(c_input, &d, &n, in_type, verbose);
}
else{
R = (unsigned char**) file_load_multiple(c_input, &d, &n, in_type, 0);
}
if(n>pow(2,30) && (sizeof(int_t)<8)){
fprintf(stderr, "####\n");
fprintf(stderr, "ERROR: INPUT LARGER THAN %.1lf GB (%.1lf GB)\n", WORD/pow(2,30), n/pow(2,30));
fprintf(stderr, "PLEASE USE %s-64\n", argv[0]);
fprintf(stderr, "####\n");
exit(EXIT_FAILURE);
}
//concatenate all string
unsigned char *T = cat_all(R, d, &n, verbose, upper);
#if DEBUG
printf("R:\n");
for(i=0; i<d && i<10; i++)
printf("%" PRIdN ") %s (%zu)\n", i, R[i], strlen((char*)R[i]));
printf("####\n");
for(i=0; i<n; i++) printf("[%d]", T[i]);
printf("\n");
#endif
//quality score sequence
unsigned char **QS;
unsigned char *qs = NULL;
if(q){
size_t n=0;
QS = (unsigned char**) file_load_multiple_qs(c_input, &d, &n, in_type);
//concatenate all string
qs = cat_all(QS, d, &n, 0, 0);
#if DEBUG
printf("QS:\n");
for(i=0; i<d && i<10; i++)
printf("%" PRIdN ") %s (%zu)\n", i, QS[i], strlen((char*)QS[i]));
printf("####\n");
for(i=0; i<n; i++) printf("[%d]", qs[i]);
printf("\n");
#endif
//free memory
for(i=0; i<d; i++)
free(QS[i]);
free(QS);
}
//free memory
for(i=0; i<d; i++)
free(R[i]);
free(R);
int_t *SA = NULL;
SA = (int_t*) malloc(n*sizeof(int_t));
assert(SA);
int_t i;
for(i=0; i<n; i++) SA[i]=0;
int_t *ISA = NULL;
if(isa){
ISA = (int_t*) malloc(n*sizeof(int_t));
assert(ISA);
}
int_t *LCP = NULL;
if(lcp || gesa || lcp_max || lcp_avg || lcp_max_text){
LCP = (int_t*) malloc(n*sizeof(int_t));
assert(LCP);
for(i=0; i<n; i++) LCP[i]=0;
}
int_da *DA = NULL;
rankbv_t* rbv = NULL;
if(da || gsa || gesa){
if(light==0){
DA = (int_da*) malloc(n*sizeof(int_da));
assert(DA);
for(i=0; i<n; i++) DA[i]=0;
}
}
if(verbose){
printf("########\n");
printf("INPUT = %s\n", c_input);
printf("OUTPUT = %s", c_output);
if(sa) printf("[.sa]");
if(isa) printf("[.isa]");
if(lcp) printf("[.lcp]");
if(da) printf("[.da]");
if(gsa) printf("[.gsa]");
if(gesa) printf("[.gesa]");
if(bwt) printf("[.bwt]");
if(q) printf("[.qs]");
printf("\n");
printf("N = %zu\n", n);
printf("d = %d\n", d);
printf("sizeof(int) = %zu bytes\n", sizeof(int_t));
if(da){
if(light) printf("DA = lightweight\n");
else printf("sizeof(int_da) = %zu bytes\n", sizeof(int_da));
}
#if TERMINATOR
printf("TERMINATOR\n");
#endif
printf("########\n");
}
/********/
printf("## gsufsort ##\n");
if(time){
time_start(&t_start, &c_start);
}
if(light){
gsacak(T, (uint_t*)SA, LCP, NULL, n);
//free LCP
if(lcp){
if(trlcp){
for(i=0; i<n; i++) if(LCP[i]>trlcp) LCP[i]=trlcp;
}
printf("## store_to_disk ##\n");
#if TERMINATOR
store_to_disk(NULL, NULL, NULL, NULL, LCP, n, c_output, "lcp", 0, 0, lcp_bytes);
#else
store_to_disk(NULL, NULL, NULL, NULL, LCP+1, n-1, c_output, "lcp", 0, 0, lcp_bytes);
#endif
}
if(lcp && !gesa && !lcp_avg && !lcp_max && !lcp_max_text && !print) free(LCP);
else if(verbose){
printf("WARNING: LCP[1,N] not freed because of: ");
if(gesa) printf("--gesa ");
if(lcp_avg) printf("--lcp_avg ");
if(lcp_max) printf("--lcp_max ");
if(lcp_max_text) printf("--lcp_max_text ");
if(print) printf("--print ");
printf("\n");
}
/**/
//compute DA
if(da || gsa || gesa){
rbv = rankbv_create(n,2);
int_t i=0;
for(;i<n-1;i++) if(T[i]==1) rankbv_setbit(rbv,i+1);
rankbv_build(rbv);
}
}
else{
gsacak(T, (uint_t*)SA, LCP, DA, n);
if(trlcp){
for(i=0; i<n; i++) if(LCP[i]>trlcp) LCP[i]=trlcp;
}
}
//compute ISA
if(isa){
int_t i=0;
for(;i<n;i++) ISA[SA[i]]=i;
}
if(time){
double d_time = time_stop(t_start, c_start);
if(verbose) fprintf(stderr,"%.6lf\n", d_time);
}
/********/
if(time){
time_start(&t_start, &c_start);
}
if(light){
if(!lcp)
printf("## store_to_disk ##\n");
}
else
printf("## store_to_disk ##\n");
#if TERMINATOR
//store to disk
if(str) store_to_disk(T, NULL, NULL, NULL, NULL, n, c_output, "str", sizeof(char), 0, 0);
if(sa) store_to_disk(NULL, NULL, NULL, SA, NULL, n, c_output, "sa", 0, sa_bytes, 0);
if(isa) store_to_disk(NULL, NULL, NULL, ISA, NULL, n, c_output, "isa", 0, isa_bytes, 0);
if(light==0)
if(lcp) store_to_disk(NULL, NULL, NULL, NULL, LCP, n, c_output, "lcp", 0, 0, lcp_bytes);
if(da) store_to_disk(NULL, DA, rbv, SA, NULL, n, c_output, "da", da_bytes, 0, 0);
if(gsa) store_to_disk(NULL, DA, rbv, SA, NULL, n, c_output, "gsa", t_bytes, s_bytes, 0);
if(gesa) store_to_disk(T, DA, rbv, SA, LCP, n, c_output, "gesa", t_bytes, s_bytes, lcp_bytes);
if(bwt) store_to_disk(T, NULL, NULL, SA, NULL, n, c_output, "bwt", sizeof(char), 0, 0);
if(q) store_to_disk(qs, NULL, NULL, SA, NULL, n, c_output, "bwt.qs", sizeof(char), 0, 0);
#else
//store to disk (+1 ignores last terminator)
if(str) store_to_disk(T, NULL, NULL, NULL, NULL, n-1, c_output, "str", sizeof(char), 0, 0);
if(sa) store_to_disk(NULL, NULL, NULL, SA+1, NULL, n-1, c_output, "sa", 0, sa_bytes, 0);
if(isa) store_to_disk(NULL, NULL, NULL, ISA+1, NULL, n-1, c_output, "isa", 0, isa_bytes, 0);
if(light==0)
if(lcp) store_to_disk(NULL, NULL, NULL, NULL, LCP+1, n-1, c_output, "lcp", 0, 0, lcp_bytes);
if(da) store_to_disk(NULL, DA+1, rbv, SA+1, NULL, n-1, c_output, "da", da_bytes, 0, 0);
if(gsa) store_to_disk(NULL, DA+1, rbv, SA+1, NULL, n-1, c_output, "gsa", t_bytes, s_bytes, 0);
if(gesa) store_to_disk(T, DA+1, rbv, SA+1, LCP+1, n-1, c_output, "gesa", t_bytes, s_bytes, lcp_bytes);
if(bwt) store_to_disk(T, NULL, NULL, SA+1, NULL, n-1, c_output, "bwt", sizeof(char), 0, 0);
if(q) store_to_disk(qs, NULL, NULL, SA+1, NULL, n-1, c_output, "bwt.qs", sizeof(char), 0, 0);
#endif
if(time){
double d_time = time_stop(t_start, c_start);
if(verbose) fprintf(stderr,"%.6lf\n", d_time);
}
/********/
if(print){
printf("## print ##\n");
if(!p)p=n;
#if TERMINATOR
print_array(T, DA, rbv, light, SA, ISA, LCP, str=1, da, sa, isa, lcp, bwt || gesa, gsa || gesa, gesa, n, min(n,p), 1);
#else
print_array(T, DA+1, rbv, light, SA+1, ISA+1, LCP+1, str=1, da, sa, isa, lcp, bwt || gesa, gsa || gesa, gesa, n-1, min(n-1,p), 0);
#endif
}
if(lcp_max || lcp_avg || lcp_max_text){
int_t max=0,total=n, j=0;
double avg=0.0;
#if TERMINATOR == 0
total=n-1;
#endif
for(i=0; i<n; i++){
if(LCP[i]>max){
max=LCP[i];
j=i;
}
avg+=(double)LCP[i]/(double)total;
}
if(lcp_max){
//printf("LCP max: %" PRIdN "\n", max);
store_to_disk(NULL, NULL, NULL, NULL, &max, 1, c_output, "lcp_max", 0, 0, lcp_bytes);
}
if(lcp_max_text){
/**
printf("Longest LCP: ");
for(i=SA[j]; i<SA[j]+max && T[i]!=1; i++){
printf("%c", T[i]-1);
}
printf("\n");
**/
store_to_disk(&T[SA[j]], NULL, NULL, NULL, NULL, SA[j]+max, c_output, "lcp_max.txt", sizeof(char), 0, 0);
}
if(lcp_avg){
//printf("LCP avg: %lf\n", avg);
int_t AVG = (int_t)avg;
store_to_disk(NULL, NULL, NULL, NULL, &AVG, 1, c_output, "lcp_avg", 0, 0, lcp_bytes);
}
}
//free memory
free(T);
if(q)
free(qs);
free(SA);
if(isa)
free(ISA);
if(light){
if(gesa || lcp_max || lcp_avg || lcp_max_text) free(LCP);
}
else{
if(lcp || gesa || lcp_max || lcp_avg || lcp_max_text) free(LCP);
}
if(da || gsa || gesa){
if(light)
rankbv_free(rbv);
else
free(DA);
}
}//if BUILD
else if(load){
printf("## load_from_disk ##\n");
if(verbose){
printf("########\n");
if(sa) printf("SA = %d bytes\n", sa_bytes);
if(isa) printf("ISA = %d bytes\n", isa_bytes);
if(lcp) printf("LCP = %d bytes\n", lcp_bytes);
if(da) printf("DA = %d bytes\n", da_bytes);
if(gsa) printf("GSA = (%d, %d) bytes\n", t_bytes, s_bytes);
if(gesa) printf("GESA = (%d, %d, %d, 1) bytes\n", t_bytes, s_bytes, lcp_bytes);
printf("########\n");
}
unsigned char *T = NULL;
unsigned char *BWT = NULL;
int_t *SA = NULL;
int_t *ISA = NULL;
int_t *LCP = NULL;
int_da *DA = NULL;
int_da *GSA_text = NULL;
int_t *GSA_suff = NULL;
size_t n=0;
if(str) n = load_from_disk(&T, NULL, NULL, NULL, c_input, "str", 1, 0, 0);
if(sa) n = load_from_disk(NULL, NULL, &SA, NULL, c_input, "sa", 0, sa_bytes, 0);
if(isa) n = load_from_disk(NULL, NULL, &ISA, NULL, c_input, "isa", 0, isa_bytes, 0);
if(lcp) n = load_from_disk(NULL, NULL, NULL, &LCP, c_input, "lcp", 0, 0, lcp_bytes);
if(da) n = load_from_disk(NULL, &DA, NULL, NULL, c_input, "da", da_bytes, 0, 0);
if(gsa) n = load_from_disk(NULL, &GSA_text, &GSA_suff, NULL, c_input, "gsa", t_bytes, s_bytes, 0);
if(gesa) n = load_from_disk(&BWT, &GSA_text, &GSA_suff, &LCP, c_input, "gesa", t_bytes, s_bytes, lcp_bytes);
if(bwt) n = load_from_disk(&BWT, NULL, NULL, NULL, c_input, "bwt", 1, 0, 0);
if(trlcp){
for(i=0; i<n; i++) if(LCP[i]>trlcp) LCP[i]=trlcp;
}
if(lcp_max || lcp_avg || lcp_max_text){
int_t max=0, j=0;
double avg=0.0;
for(i=0; i<n; i++){
if(LCP[i]>max){
max=LCP[i];
j=i;
}
avg+=(double)LCP[i]/(double)n;
}
if(lcp_max) printf("LCP max: %" PRIdN "\n", max);
if(lcp_max_text){
if(LCP && SA && T){
printf("Longest LCP: ");
for(i=SA[j]; i<SA[j]+max && T[i]!=1; i++){
printf("%c", T[i]);
}
printf("\n");
}
else{
printf("ERROR: --lcp_max_text needs --str, --sa and --lcp.\n");
}
}
if(lcp_avg) printf("LCP avg: %lf\n", avg);
}
if(print){
printf("## print ##\n");
// output
printf("i\t");
if(sa) printf("SA\t");
if(isa) printf("ISA\t");
if(da) printf("DA\t");
if(gsa) printf("GSA\t\t");
if(gesa) printf("GESA\t\t");
if(LCP) printf("LCP\t");
if(bwt || gesa) printf("BWT\t");
if(str) printf("suffixes");
printf("\n");
if(!p)p=n;
for(i = 0; i < min(n,p); ++i) {
printf("%" PRIdN "\t",i);
if(sa) printf("%" PRIdN "\t",SA[i]);
if(isa) printf("%" PRIdN "\t",ISA[i]);
if(da) printf("%" PRIdA "\t",DA[i]);
if(gsa || gesa) printf("(%" PRIdA ", %" PRIdN ") \t", GSA_text[i], GSA_suff[i]);
if(LCP) printf("%" PRIdN "\t",LCP[i]);
if(bwt || gesa){
if(BWT[i]==terminator)
printf("#\t");
else if (BWT[i]==separator)
printf("$\t");
else
printf("%c\t",BWT[i]);
}
if(str && sa){
int_t j=SA[i];
while(j<n){
if(T[j]=='\n'){ printf("$"); break;}
else printf("%c", T[j]);
j++;
}
}
printf("\n");
}
}
if(str) free(T);
if(bwt) free(BWT);
if(sa) free(SA);
if(isa) free(ISA);
if(lcp) free(LCP);
if(da) free(DA);
if(gsa){
free(GSA_text);
free(GSA_suff);
}
}
else if(ibwt){
printf("## inverse_bwt ##\n");
unsigned char *BWT = NULL;
unsigned char *T = NULL;
size_t n = load_from_disk(&BWT, NULL, NULL, NULL, c_input, "ibwt", 1, 0, 0);
//compute LF
size_t i;
int C[SIGMA];
for(i=0; i<SIGMA; i++) C[i]=0;
for(i=0; i<n; i++) C[BWT[i]]++;
size_t sum=0;
for(i=0; i<SIGMA; i++){
sum+=C[i];
C[i]=sum-C[i];
}
size_t docs=0;
int_t *LF = (int_t*) malloc(n*sizeof(int_t));
for(i=0; i<n; i++){
LF[i] = C[BWT[i]]++;
if(BWT[i]==separator)//separator
docs++;
}
T = (unsigned char*) malloc(n*sizeof(unsigned char));
//TODO --qs
unsigned char *QS = NULL;
unsigned char *qs = NULL;
if(q){
if(load_from_disk(&QS, NULL, NULL, NULL, c_input, "qs", 1, 0, 0)!=n)
exit(EXIT_FAILURE);
qs = (unsigned char*) malloc(n*sizeof(unsigned char));
}
size_t j;
#if TERMINATOR
j=0;
docs++;
#else
j=--docs;
#endif
for(i=2; i <n+1; i++){
T[n-i]= (BWT[j]>separator)?BWT[j]:'\n';
if(q) qs[n-i]=(QS[j]>separator)?QS[j]:'\n';
//augmented LF-mapping
if(BWT[j]==separator) j=--docs;
else j=LF[j];
}
T[n-1]='\n';
if(q) qs[n-1]='\n';
if(print)
printf("%s\n", T);
printf("## store_to_disk ##\n");
#if TERMINATOR
store_to_disk(T, NULL, NULL, NULL, NULL, n-1, (c_output), "ibwt", sizeof(char), 0, 0);
if(q)
store_to_disk(qs, NULL, NULL, NULL, NULL, n-1, (c_output), "iqs", sizeof(char), 0, 0);
#else
store_to_disk(T, NULL, NULL, NULL, NULL, n, (c_output), "ibwt", sizeof(char), 0, 0);
if(q)
store_to_disk(qs, NULL, NULL, NULL, NULL, n, (c_output), "iqs", sizeof(char), 0, 0);
#endif
free(BWT);
free(T);
free(LF);
if(q){
free(QS);
free(qs);
}
}
if(time){
printf("## total ##\n");
double d_time = time_stop(t_total, c_total);
if(verbose) fprintf(stderr,"%.6lf\n", d_time);
}
if(!output)
free(c_output);
return 0;
}
/******************************************************************************/
int store_to_disk(unsigned char *T, int_da *DA, rankbv_t* rbv, int_t *SA, int_t *LCP, size_t n, char* c_file, char *ext, int wsize1, int wsize2, int wsize3){
char c_out[256];
if(strcmp(ext, "gsa")==0)
sprintf(c_out, "%s.%d.%d.%s", c_file, wsize1, wsize2, ext);
else if(strcmp(ext, "gesa")==0)
sprintf(c_out, "%s.%d.%d.%d.1.%s", c_file, wsize1, wsize2, wsize3, ext);
else if(strcmp(ext, "da")==0)
sprintf(c_out, "%s.%d.%s", c_file, wsize1, ext);
else if(strcmp(ext, "sa")==0 || strcmp(ext, "isa")==0)
sprintf(c_out, "%s.%d.%s", c_file, wsize2, ext);
else if(strcmp(ext, "lcp")==0)
sprintf(c_out, "%s.%d.%s", c_file, wsize3, ext);
else if(strcmp(ext, "bwt")==0 || strcmp(ext, "ibwt")==0 || strcmp(ext, "bwt.qs")==0|| strcmp(ext, "iqs")==0 || strcmp(ext, "lcp_max.txt")==0)
sprintf(c_out, "%s.%s", c_file, ext);
else if(strcmp(ext, "lcp_avg")==0 || strcmp(ext, "lcp_max")==0)
sprintf(c_out, "%s.%d.%s", c_file, wsize3, ext);
else
sprintf(c_out, "%s.%d.%s", c_file, wsize1, ext);
FILE *f_out = NULL;
if(strcmp(ext, "str")==0 || strcmp(ext, "bwt")==0 || strcmp(ext, "ibwt")==0 || strcmp(ext, "bwt.qs")==0|| strcmp(ext, "iqs")==0 || strcmp(ext, "lcp_max.txt"))
f_out = file_open(c_out, "w");
else
f_out = file_open(c_out, "wb");
size_t wsize = wsize1+wsize2+wsize3;
if(strcmp(ext, "gesa")==0) wsize++;
printf("%s \t%zu bytes (n = %zu)\n", c_out, n*wsize, n);
size_t i;
if(strcmp(ext, "gsa")==0){
for(i=0; i<n; i++){
int_t da_value = (light)?rankbv_rank1(rbv,SA[i]):DA[i];
fwrite(&da_value, wsize1, 1, f_out);
#if TERMINATOR
int_t value = (da_value==0)?SA[i]:SA[i]-SA[da_value]-1;
#else
int_t value = (da_value==0)?SA[i]:SA[i]-SA[da_value-1]-1;
#endif
fwrite(&value, wsize2, 1, f_out);
}
}
else if(strcmp(ext, "gesa")==0){
for(i=0; i<n; i++){
//GSA
int_t da_value = (light)?rankbv_rank1(rbv,SA[i]):DA[i];
fwrite(&da_value, wsize1, 1, f_out);
#if TERMINATOR
int_t value = (da_value==0)?SA[i]:SA[i]-SA[da_value]-1;
#else
int_t value = (da_value==0)?SA[i]:SA[i]-SA[da_value-1]-1;
#endif
fwrite(&value, wsize2, 1, f_out);
//LCP
fwrite(&LCP[i], wsize3, 1, f_out); //LCP==C
//BWT
#if TERMINATOR
char c = (!SA[i])?terminator:((T[SA[i]-1]>1)?T[SA[i]-1]-1:separator); //separators = 1, and terminator = 0
#else
char c = (!SA[i])?separator:((T[SA[i]-1]>1)?T[SA[i]-1]-1:separator); //separators = 0, no terminator
#endif
fwrite(&c, sizeof(char), 1, f_out);
}
}
else if(strcmp(ext, "bwt")==0){
for(i=0; i<n; i++){ //SA==B
#if TERMINATOR
char c = (!SA[i])?terminator:((T[SA[i]-1]>1)?T[SA[i]-1]-1:separator); //separators = 1, and terminator = 0
#else
char c = (!SA[i])?separator:((T[SA[i]-1]>1)?T[SA[i]-1]-1:separator); //separators = 0, no terminator
#endif
fwrite(&c, wsize1, 1, f_out);
}
}
else if(strcmp(ext, "bwt.qs")==0){
for(i=0; i<n; i++){ //SA==B
#if TERMINATOR
char c = (!SA[i])?terminator:((T[SA[i]-1]>1)?T[SA[i]-1]-1:separator); //separators = 1, and terminator = 0
#else
char c = (!SA[i])?separator:((T[SA[i]-1]>1)?T[SA[i]-1]-1:separator); //separators = 0, no terminator
#endif
fwrite(&c, wsize1, 1, f_out);
}
}
else if(strcmp(ext, "str")==0){
for(i=0; i<n; i++){
char c = (T[i]>0)?T[i]-1:'\n';
if(c==0) c = '\n';
fwrite(&c, wsize1, 1, f_out);
}
}
else if(strcmp(ext, "da")==0){
for(i=0; i<n; i++){
int_t da_value = (light)?rankbv_rank1(rbv,SA[i]):DA[i];
fwrite(&da_value, wsize1, 1, f_out);
}
}
else if(strcmp(ext, "sa")==0){
for(i=0; i<n; i++){
fwrite(&SA[i], wsize2, 1, f_out);
}
}
else if(strcmp(ext, "isa")==0){
for(i=0; i<n; i++){
fwrite(&SA[i], wsize2, 1, f_out);
}
}
else if(strcmp(ext, "lcp")==0){
for(i=0; i<n; i++){
fwrite(&LCP[i], wsize3, 1, f_out);
}
}
else if(strcmp(ext, "ibwt")==0 || strcmp(ext, "iqs")==0){
fwrite(T, wsize1, n, f_out);
}
else if(strcmp(ext, "lcp_avg")==0 || strcmp(ext, "lcp_max")==0){
fwrite(LCP, wsize3, 1, f_out);
}
else if(strcmp(ext, "lcp_max.txt")==0){
for(i=0; i<n && T[i]!=1 ; i++){
char c = (T[i]>0)?T[i]-1:'\n';
if(c==0) c = '\n';
fwrite(&c, wsize1, 1, f_out);
}
}
file_close(f_out);
return 0;
}
/******************************************************************************/
size_t load_from_disk(unsigned char **T, int_da **DA, int_t **SA, int_t **LCP, char* c_file, char *ext, int wsize1, int wsize2, int wsize3){
char c_in[256];
if(strcmp(ext, "gsa")==0)
sprintf(c_in, "%s.%d.%d.%s", c_file, wsize1, wsize2, ext);
else if(strcmp(ext, "gesa")==0)
sprintf(c_in, "%s.%d.%d.%d.1.%s", c_file, wsize1, wsize2, wsize3, ext);
else if(strcmp(ext, "da")==0)
sprintf(c_in, "%s.%d.%s", c_file, wsize1, ext);
else if(strcmp(ext, "sa")==0 || strcmp(ext, "isa")==0)
sprintf(c_in, "%s.%d.%s", c_file, wsize2, ext);
else if(strcmp(ext, "lcp")==0)
sprintf(c_in, "%s.%d.%s", c_file, wsize3, ext);
else if(strcmp(ext, "ibwt")==0)
sprintf(c_in, "%s", c_file);
else if(strcmp(ext, "bwt")==0 || strcmp(ext, "qs")==0)
sprintf(c_in, "%s.%s", c_file, ext);
else
sprintf(c_in, "%s.%d.%s", c_file, wsize1, ext);
FILE *f_in=NULL;
if(strcmp(ext, "str")==0 || strcmp(ext, "bwt")==0 || strcmp(ext, "ibwt")==0 || strcmp(ext, "bwt.qs")==0|| strcmp(ext, "iqs")==0)
f_in = file_open(c_in, "r");
else
f_in = file_open(c_in, "rb");
if(f_in==NULL){
exit(EXIT_FAILURE);
}
size_t size = file_size(f_in);
size_t wsize = wsize1+wsize2+wsize3;
if(strcmp(ext, "gesa")==0) wsize++;
size_t n = size/wsize;
printf("%s\t%zu bytes (n = %zu)\n", c_in, size, n);
if(strcmp(ext, "str")==0 || strcmp(ext, "bwt")==0 || strcmp(ext, "ibwt")==0 || strcmp(ext, "qs")==0){
*T= (unsigned char*) malloc(n*sizeof(unsigned char));
if(fread(*T, wsize1, n, f_in)==EOF)
perror("main_t");
}
else{
if(DA!=NULL){
*DA = (int_da*) malloc(n*sizeof(int_da));
}
if(SA!=NULL){
*SA = (int_t*) malloc(n*sizeof(int_t));
}
if(LCP!=NULL){
*LCP = (int_t*) malloc(n*sizeof(int_t));
}
if(strcmp(ext, "gesa")==0){
*T= (unsigned char*) malloc(n*sizeof(unsigned char));
}
size_t i;
for(i=0; i<n; i++){
if(DA){
int_da da_value=0;
if(fread(&da_value, wsize1, 1, f_in)==EOF)
perror("main_da_value");
(*DA)[i] = (int_da) da_value;
}
int_t value=0;
if(SA){
if(fread(&value, wsize2, 1, f_in)==EOF)
perror("main_sa_value");
(*SA)[i] = (int_t) value;
}
//LCP (gesa)
if(LCP){
if(fread(&value, wsize3, 1, f_in)==EOF)
perror("main_lcp_value");
(*LCP)[i] = (int_t) value;
}
//BWT (gesa)
if(strcmp(ext, "gesa")==0){
if(fread(&value, sizeof(char), 1, f_in)==EOF)
perror("main_gesa_value");
(*T)[i] = (char) value;