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bwt.cpp
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bwt.cpp
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// This is a demo program for showing how to call SACA_K.
#include<stdio.h>
#include<stdint.h>
#include <stdlib.h>
#include <time.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <sys/time.h>
#include <time.h>
#include "bwt.h"
#include<stdint.h>
#include<ctype.h>
#include <unistd.h>
///#include <nmmintrin.h>
bwt_index bitmapper_index_params;
SA_block build_sa_block;
unsigned int debug_2 = 0;
unsigned int debug_total = 0;
void dec_bit_bwt(bwt_string_type input)
{
unsigned int bit_2[64];
int i = 0;
for (i = 0; i < 64; i++)
{
bwt_string_type tmp = (bwt_string_type)((bwt_string_type)input&(bwt_string_type)1);
input = input >> 1;
if (tmp == (bwt_string_type)0)
{
bit_2[i] = 0;
}
else
{
bit_2[i] = 1;
}
}
for (i = 63; i >= 0; i--)
{
fprintf(stderr, "%u", bit_2[i]);
}
fprintf(stderr, "\n");
}
void SACA_K(unsigned char *s, unsigned int *SA, unsigned int n,
unsigned int K, unsigned int m, int level);
inline void bwt_direct_get_sa_interval_long_back_up_1
(SA_flag_string_type* SA_flag, unsigned int sp, unsigned int ep, unsigned int* start, unsigned int* length)
{
unsigned int j_sp, j_ep;
unsigned int l;
unsigned int i = 0;
unsigned int last_sp, last_ep;
unsigned int actually_line_sp, actually_line_ep;
unsigned int ans_sp, ans_ep, flag;
SA_flag_string_type tmp_SA_pop_count;
flag = 0;
l = sp;
///这是除以224，乘以256，最后再除以64，这就是确定属于哪个block
actually_line_sp = ((l / bitmapper_index_params.compress_SA_flag) << 8) >> 6;
///这是对224取余，这就是确定block内部还需要扫描的位数
last_sp = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
l = ep;
///这是除以224，乘以256，最后再除以64，这就是确定属于哪个block
actually_line_ep = ((l / bitmapper_index_params.compress_SA_flag) << 8) >> 6;
///这是除以224，乘以256，最后再除以64，这就是确定属于哪个block
last_ep = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
///这说明sp和ep在同一个block内部,则count操作可以部分重叠
if (actually_line_sp == actually_line_ep)
{
flag = 1;
}
ans_sp = SA_flag[actually_line_sp] >> bitmapper_index_params.SA_counter_shift_length;
if (last_sp != 0)
{
///主要last本身已经加过SA_counter_length了, 所以这里j=0, 否则就应该把j = SA_counter_length
j_sp = 0;
tmp_SA_pop_count = SA_flag[actually_line_sp] & bitmapper_index_params.SA_pop_count_mode;
while (j_sp + bitmapper_index_params.SA_flag_warp_number <= last_sp)
{
ans_sp = ans_sp + __builtin_popcountll(tmp_SA_pop_count);
j_sp = j_sp + bitmapper_index_params.SA_flag_warp_number;
actually_line_sp++;
tmp_SA_pop_count = SA_flag[actually_line_sp];
}
///这个判断条件貌似是sp和ep都属于同一个block
///所以ep的值貌似可以直接继承
if (flag == 1)
{
j_ep = j_sp;
ans_ep = ans_sp;
actually_line_ep = actually_line_sp;
flag = 2;
}
last_sp = last_sp - j_sp;
if (last_sp != 0)
{
ans_sp = ans_sp +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last_sp))));
}
}
(*start) = ans_sp;
if (last_ep != 0)
{
if (flag==2)
{
tmp_SA_pop_count = SA_flag[actually_line_ep];
while (j_ep + bitmapper_index_params.SA_flag_warp_number <= last_ep)
{
ans_ep = ans_ep + __builtin_popcountll(tmp_SA_pop_count);
j_ep = j_ep + bitmapper_index_params.SA_flag_warp_number;
actually_line_ep++;
tmp_SA_pop_count = SA_flag[actually_line_ep];
}
last_ep = last_ep - j_ep;
if (last_ep != 0)
{
ans_ep = ans_ep +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last_ep))));
}
}
else
{
ans_ep = SA_flag[actually_line_ep] >> bitmapper_index_params.SA_counter_shift_length;
///主要last本身已经加过SA_counter_length了，所以这里j=0；否则就应该把j = SA_counter_length
j_ep = 0;
tmp_SA_pop_count = SA_flag[actually_line_ep] & bitmapper_index_params.SA_pop_count_mode;
while (j_ep + bitmapper_index_params.SA_flag_warp_number <= last_ep)
{
ans_ep = ans_ep + __builtin_popcountll(tmp_SA_pop_count);
j_ep = j_ep + bitmapper_index_params.SA_flag_warp_number;
actually_line_ep++;
tmp_SA_pop_count = SA_flag[actually_line_ep];
}
last_ep = last_ep - j_ep;
if (last_ep != 0)
{
ans_ep = ans_ep +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last_ep))));
}
}
}
else
{
ans_ep = SA_flag[actually_line_ep] >> bitmapper_index_params.SA_counter_shift_length;
}
(*length) = ans_ep - (*start);
}
inline void bwt_direct_get_sa_interval_long
(SA_flag_string_type* SA_flag,
bitmapper_bs_iter sp,
bitmapper_bs_iter ep,
bitmapper_bs_iter* start,
bitmapper_bs_iter* length)
{
bitmapper_bs_iter last_sp, last_ep;
bitmapper_bs_iter actually_line_sp, actually_line_ep;
bitmapper_bs_iter ans_sp, ans_ep;
bitmapper_bs_iter j_sp, j_ep;
bitmapper_bs_iter flag = 0;
SA_flag_string_type tmp_SA_pop_count;
actually_line_sp = ((sp >> 8 ) * bitmapper_index_params.acctuall_SA_flag_gap) >> 6;
last_sp = sp & 255;
actually_line_ep = ((ep >> 8 ) * bitmapper_index_params.acctuall_SA_flag_gap) >> 6;
last_ep = ep & 255;
if (actually_line_sp == actually_line_ep)
{
flag = 1;
}
ans_sp = SA_flag[actually_line_sp];
if (last_sp != 0)
{
///主要last本身已经加过SA_counter_length了，所以这里j=0；否则就应该把j = SA_counter_length
j_sp = 0;
actually_line_sp++;
tmp_SA_pop_count = SA_flag[actually_line_sp];
while (j_sp + bitmapper_index_params.SA_flag_warp_number <= last_sp)
{
ans_sp = ans_sp + __builtin_popcountll(tmp_SA_pop_count);
j_sp = j_sp + bitmapper_index_params.SA_flag_warp_number;
actually_line_sp++;
tmp_SA_pop_count = SA_flag[actually_line_sp];
}
if (flag == 1)
{
ans_ep = ans_sp;
j_ep = j_sp;
actually_line_ep = actually_line_sp;
flag = 2;
}
last_sp = last_sp - j_sp;
if (last_sp != 0)
{
ans_sp = ans_sp +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last_sp))));
}
}
(*start) = ans_sp;
if (last_ep != 0)
{
if (flag == 2)
{
while (j_ep + bitmapper_index_params.SA_flag_warp_number <= last_ep)
{
ans_ep = ans_ep + __builtin_popcountll(tmp_SA_pop_count);
j_ep = j_ep + bitmapper_index_params.SA_flag_warp_number;
actually_line_ep++;
tmp_SA_pop_count = SA_flag[actually_line_ep];
}
last_ep = last_ep - j_ep;
if (last_ep != 0)
{
ans_ep = ans_ep +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last_ep))));
}
}
else
{
ans_ep = SA_flag[actually_line_ep];
actually_line_ep++;
j_ep = 0;
tmp_SA_pop_count = SA_flag[actually_line_ep];
while (j_ep + bitmapper_index_params.SA_flag_warp_number <= last_ep)
{
ans_ep = ans_ep + __builtin_popcountll(tmp_SA_pop_count);
j_ep = j_ep + bitmapper_index_params.SA_flag_warp_number;
actually_line_ep++;
tmp_SA_pop_count = SA_flag[actually_line_ep];
}
last_ep = last_ep - j_ep;
if (last_ep != 0)
{
ans_ep = ans_ep +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last_ep))));
}
}
}
else
{
ans_ep = SA_flag[actually_line_ep];
}
(*length) = ans_ep - (*start);
}
inline void bwt_direct_get_sa_interval_long_back_up
(SA_flag_string_type* SA_flag, unsigned int sp, unsigned int ep, unsigned int* start, unsigned int* length)
{
unsigned int l;
unsigned int i = 0;
///uint64_t tmp_SA_flag;
unsigned int last;
unsigned int actually_line;
unsigned int ans;
SA_flag_string_type tmp_SA_pop_count;
l = sp;
/**
actually_line = ((l / bitmapper_index_params.compress_SA_flag)
*bitmapper_index_params.acctuall_SA_flag_gap) / bitmapper_index_params.SA_flag_warp_number;
**/
actually_line = ((l / bitmapper_index_params.compress_SA_flag) << 8) >> 6;
///这里SA要改
///last = l % compress_SA_flag;
///last = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
last = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
///这里SA要改
///ans = SA_flag[actually_line];
ans = SA_flag[actually_line] >> bitmapper_index_params.SA_counter_shift_length;
if (last != 0)
{
///主要last本身已经加过SA_counter_length了，所以这里j=0；否则就应该把j = SA_counter_length
unsigned int j = 0;
tmp_SA_pop_count = SA_flag[actually_line] & bitmapper_index_params.SA_pop_count_mode;
while (j + bitmapper_index_params.SA_flag_warp_number <= last)
{
ans = ans + __builtin_popcountll(tmp_SA_pop_count);
j = j + bitmapper_index_params.SA_flag_warp_number;
actually_line++;
tmp_SA_pop_count = SA_flag[actually_line];
}
last = last - j;
if (last != 0)
{
ans = ans +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last))));
}
}
(*start) = ans;
l = ep;
/**
actually_line = ((l / bitmapper_index_params.compress_SA_flag)
*bitmapper_index_params.acctuall_SA_flag_gap) / bitmapper_index_params.SA_flag_warp_number;
**/
actually_line = ((l / bitmapper_index_params.compress_SA_flag) << 8) >> 6;
///这里SA要改
///last = l % compress_SA_flag;
last = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
///这里SA要改
///ans = SA_flag[actually_line];
ans = SA_flag[actually_line] >> bitmapper_index_params.SA_counter_shift_length;
if (last != 0)
{
///主要last本身已经加过SA_counter_length了，所以这里j=0；否则就应该把j = SA_counter_length
unsigned int j = 0;
tmp_SA_pop_count = SA_flag[actually_line] & bitmapper_index_params.SA_pop_count_mode;
while (j + bitmapper_index_params.SA_flag_warp_number <= last)
{
ans = ans + __builtin_popcountll(tmp_SA_pop_count);
j = j + bitmapper_index_params.SA_flag_warp_number;
actually_line++;
tmp_SA_pop_count = SA_flag[actually_line];
}
last = last - j;
if (last != 0)
{
ans = ans +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last))));
}
}
(*length) = ans - (*start);
}
inline unsigned int bwt_get_sa_restrict_steps_less_than_4
(SA_flag_string_type* SA_flag, unsigned int line,
bwt_string_type *bwt, high_occ_table_type* high_occ_table,
unsigned int *sa, unsigned int need_step, unsigned int* accessed_sa)
{
unsigned int l = line;
bwt_string_type delta;
unsigned int i = 0;
if (line == bitmapper_index_params.shapline) return 0;
unsigned int actually_line;
unsigned int last;
/**
///这里SA要改
unsigned int actually_line = ((l / bitmapper_index_params.compress_SA_flag)
*bitmapper_index_params.acctuall_SA_flag_gap) / bitmapper_index_params.SA_flag_warp_number;
///这里SA要改
///unsigned int last = l % compress_SA_flag;
unsigned int last = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
actually_line = actually_line + last / bitmapper_index_params.SA_flag_warp_number;
**/
actually_line = ((l / bitmapper_index_params.compress_SA_flag) << 8) >> 6;
last = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
actually_line = actually_line + (last >> 6);
/**
while (((SA_flag[actually_line] << (last % bitmapper_index_params.SA_flag_warp_number))
&bitmapper_index_params.mode_SA_flag) == 0)
**/
while (((SA_flag[actually_line] << (last & 63))&bitmapper_index_params.mode_SA_flag) == 0)
{
if (i >= need_step)
{
return 0;
}
/**
///似乎只有这里要改，因为这里涉及到取BWT了
///这里做了修改
///actually_line = ((l / compress_occ)*acctuall_bwt_gap) + l % compress_occ + 64;
actually_line = ((l / bitmapper_index_params.compress_occ)
*bitmapper_index_params.acctuall_bwt_gap) + l % bitmapper_index_params.compress_occ + 32;
delta = (bwt[actually_line / bitmapper_index_params.bwt_warp_number]
>> ((bitmapper_index_params.bwt_warp_number - actually_line%bitmapper_index_params.bwt_warp_number - 1) * 2))
&(bwt_string_type)3;
**/
actually_line = ((l >> 8)*bitmapper_index_params.acctuall_bwt_gap) + (l & 255) + 32;
/**
delta = (bwt[(actually_line >> 5)]
>> ((bitmapper_index_params.bwt_warp_number - (actually_line & 31) - 1) * 2))
&(bwt_string_type)3;
**/
delta = (bwt[(actually_line >> 5)]
>> ((bitmapper_index_params.bwt_warp_number - (actually_line & 31) - 1) << 1))
&(bwt_string_type)3;
l = find_occ_fm_index(l, delta, bwt, high_occ_table);
i++;
if (l == bitmapper_index_params.shapline)
{
(*accessed_sa) = i;
return i;
}
/**
///这里SA要改
///actually_line = ((l / compress_SA_flag)*acctuall_SA_flag_gap) / SA_flag_warp_number + 1;
actually_line = ((l / bitmapper_index_params.compress_SA_flag)*bitmapper_index_params.acctuall_SA_flag_gap)
/ bitmapper_index_params.SA_flag_warp_number;
///这里SA要改
///last = l % compress_SA_flag;
last = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
actually_line = actually_line + last / bitmapper_index_params.SA_flag_warp_number;
**/
actually_line = ((l / bitmapper_index_params.compress_SA_flag) << 8) >> 6;
last = l % bitmapper_index_params.compress_SA_flag + SA_counter_length;
actually_line = actually_line + (last >> 6);
}
/**
actually_line
= ((l / bitmapper_index_params.compress_SA_flag)*
bitmapper_index_params.acctuall_SA_flag_gap) / bitmapper_index_params.SA_flag_warp_number;
**/
actually_line = actually_line - (last >> 6);
///这里SA要改
///unsigned int ans = SA_flag[actually_line];
unsigned int ans = SA_flag[actually_line] >> bitmapper_index_params.SA_counter_shift_length;
///这里SA要改
if (last != 0)
{
///主要last本身已经加过SA_counter_length了，所以这里j=0；否则就应该把j = SA_counter_length
unsigned int j = 0;
SA_flag_string_type tmp_SA_pop_count;
tmp_SA_pop_count = SA_flag[actually_line] & bitmapper_index_params.SA_pop_count_mode;
while (j + bitmapper_index_params.SA_flag_warp_number <= last)
{
ans = ans + __builtin_popcountll(tmp_SA_pop_count);
j = j + bitmapper_index_params.SA_flag_warp_number;
actually_line++;
tmp_SA_pop_count = SA_flag[actually_line];
}
last = last - j;
if (last != 0)
{
ans = ans +
__builtin_popcountll((SA_flag_string_type)(tmp_SA_pop_count
& (bitmapper_index_params.mode << (bitmapper_index_params.SA_flag_warp_number - last))));
}
}
(*accessed_sa) = sa[ans] + i;
return 1;
}
inline void bwt_accesss_SA_cur_more_than_3(
unsigned int *sa, SA_flag_string_type* SA_flag, bwt_string_type *bwt, high_occ_table_type* high_occ_table,
bitmapper_bs_iter* locates,///unsigned int* locates,
bitmapper_bs_iter sp,
bitmapper_bs_iter ep,
bitmapper_bs_iter occ,
bitmapper_bs_iter* tmp_SA_length,
bitmapper_bs_iter need_step)
{
bitmapper_bs_iter t;
for (t = sp; t<ep; t++)
{
///这里SA要改
if (bwt_get_sa_restrict_steps_more_than_3(SA_flag, t, bwt, high_occ_table, sa,
need_step, (&(locates[(*tmp_SA_length)]))) == 1)
{
locates[(*tmp_SA_length)] = locates[(*tmp_SA_length)] + occ;
(*tmp_SA_length)++;
}
}
}
inline void bwt_accesss_SA_cur_less_than_4(unsigned int *sa, SA_flag_string_type* SA_flag, bwt_string_type *bwt, high_occ_table_type* high_occ_table,
unsigned int* locates,
unsigned int sp, unsigned int ep, unsigned int occ,
unsigned int* tmp_SA_length, unsigned int need_step)
{
unsigned int t;
for (t = sp; t<ep; t++)
{
///这里SA要改
if (bwt_get_sa_restrict_steps_less_than_4(SA_flag, t, bwt, high_occ_table, sa,
need_step, (&(locates[(*tmp_SA_length)]))) == 1)
{
locates[(*tmp_SA_length)] = locates[(*tmp_SA_length)] + occ;
(*tmp_SA_length)++;
}
}
}
void read_n_uint40_from_file(uint40* tab, long length, char* fname)
{
FILE *f = fopen(fname, "r");
size_t fread_ret = fread(tab, sizeof(uint40), length, f);
if ((long)fread_ret != length) {
fprintf(stderr, "\nError: fread: fread_ret=%lld, length=%lld\n",
fread_ret, length);
exit(EXIT_FAILURE);
}
fclose(f);
}
void pure_read_n_uint40_from_file(uint40* tab, long length, bitmapper_bs_iter start)
{
fseek(build_sa_block.f_sa, start*sizeof(uint40), SEEK_SET);
size_t fread_ret = fread(tab, sizeof(uint40), length, build_sa_block.f_sa);
}
void pSAscan_indenpendent_get_sa_fromFILE(uint40 **sa, unsigned int text_length, char *refer)
{
FILE* tmp_SA = fopen("tmp_ref.tmp", "w");
fwrite(refer, sizeof(char), text_length, tmp_SA);
fflush(tmp_SA);
fclose(tmp_SA);
int error=system("./psascan tmp_ref.tmp -m 8192");
error = system("rm tmp_ref.tmp");
////fprintf(stderr, "error=%d\n", error);
uint40* SA = new uint40[text_length + 1];
SA[0] = uint40(text_length, 0);
read_n_uint40_from_file(SA+1, text_length, "tmp_ref.tmp.sa5");
*sa = SA;
fclose(tmp_SA);
}
uint40 get_sa_block(bitmapper_bs_iter iter)
{
///fprintf(stderr, "iter=%llu, build_sa_block.start=%llu, build_sa_block.endl=%llu\n", iter, build_sa_block.start, build_sa_block.endl);
if (iter >= build_sa_block.start
&&
iter <= build_sa_block.endl)
{
iter = iter - build_sa_block.start;
return build_sa_block.sa_block[iter];
}
else
{
if (iter == 0)
{
build_sa_block.sa_block[0] = uint40(build_sa_block.text_length);
build_sa_block.start = 0;
build_sa_block.endl = build_sa_block.start + build_sa_block.block_size - 1;
pure_read_n_uint40_from_file(build_sa_block.sa_block+1, build_sa_block.block_size - 1, 0);
}
else
{
build_sa_block.start = iter;
build_sa_block.endl = build_sa_block.start + build_sa_block.block_size - 1;
pure_read_n_uint40_from_file(build_sa_block.sa_block, build_sa_block.block_size, iter - 1);
}
iter = iter - build_sa_block.start;
return build_sa_block.sa_block[iter];
}
}
void init_SA_block(bitmapper_bs_iter text_length)
{
build_sa_block.block_size = 1000000;
build_sa_block.text_length = text_length;
build_sa_block.sa_block = new uint40[build_sa_block.block_size];
build_sa_block.f_sa = fopen("tmp_ref.tmp.sa5", "r");
bitmapper_bs_iter file_length = 0;
fseek(build_sa_block.f_sa, 0, SEEK_END);
file_length = ftell(build_sa_block.f_sa);
fseek(build_sa_block.f_sa, 0, SEEK_SET);
file_length = file_length / sizeof(uint40);
if (text_length == file_length)
{
fprintf(stderr, "text_length =%llu, file_length=%llu\n", text_length, file_length);
fprintf(stderr, "text_length = file_length...sucess...\n");
fflush(stderr);
}
else
{
fprintf(stderr, "text_length =%llu, file_length=%llu\n", text_length, file_length);
fprintf(stderr, "ERROR: text_length != file_length...exit...\n");
fflush(stderr);
exit(0);
}
build_sa_block.sa_block[0] = uint40(text_length);
build_sa_block.start = 0;
build_sa_block.endl = build_sa_block.start + build_sa_block.block_size - 1;
pure_read_n_uint40_from_file(build_sa_block.sa_block+1, build_sa_block.block_size-1, 0);
}
void indenpendent_get_sa_fromFILE(unsigned int **sa, unsigned int cc, char *refer)
{
unsigned int i;
unsigned int n;
n = cc-1;
fprintf(stderr, "r_n=%u\n", n);
n++; // append the virtual sentinel
fprintf(stderr, "Allocating input and output space: %u bytes = %.2lf MB", 5 * n, (double)5 * n / 1024 / 1024);
unsigned char *s_ch = new unsigned char[n];
//unsigned char *s_ch;
unsigned int *SA = new unsigned int[n];
//unsigned int *SA;
///SA = (unsigned int*)malloc(sizeof(unsigned int)*n+10);
if (s_ch == NULL || SA == NULL) {
delete[] s_ch; delete[] SA;
fprintf(stderr, "\nInsufficient memory, exit!");
return;
}
// read the string into buffer.
fprintf(stderr, "\nReading input string...");
fseek(stdin, 0, SEEK_SET);
for(i=0;i<n;i++) s_ch[i]=refer[i];
// set the virtual sentinel
s_ch[n - 1] = 0;
clock_t start, finish;
double duration;
start = clock();
fprintf(stderr, "\nConstructing the suffix array...");
SACA_K(s_ch, SA, n, 256, n, 0);
finish = clock();
duration = (double)(finish - start) / CLOCKS_PER_SEC;