710 lines
24 KiB
C++
710 lines
24 KiB
C++
#include <iostream>
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#include <stdint.h>
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#include <stdlib.h>
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#include <vector>
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#include <sys/time.h>
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#include <string>
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#include <stdio.h>
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#include <algorithm>
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#include <string.h>
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#include <immintrin.h>
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#include "util.h"
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#include "bwt.h"
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#include "fmt_index.h"
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using namespace std;
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double t1 = 0, t2 = 0, t3 = 0, t4 = 0, t5 = 0, t6 = 0, t7 = 0, t8 = 0, t9 = 0, t10 = 0,
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t11 = 0, t12 = 0, t13 = 0, t14 = 0;
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long f1 = 0, f2 = 0, f3 = 0, f4 = 0, f5 = 0;
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const static char BASE[4] = {'A', 'C', 'G', 'T'};
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// 求反向互补序列
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string calc_reverse_seq(string &seq)
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{
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string rseq(seq.size(), '0');
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for (size_t i = 0; i < seq.size(); ++i)
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{
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if (seq[i] == 'A')
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rseq[i] = 'T';
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else if (seq[i] == 'C')
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rseq[i] = 'G';
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else if (seq[i] == 'G')
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rseq[i] = 'C';
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else if (seq[i] == 'T')
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rseq[i] = 'A';
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}
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std::reverse(rseq.begin(), rseq.end());
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return rseq;
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}
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// 打印32位整型数据中包含的pre-bwt：bwt
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void print_base_uint32(uint32_t p)
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{
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for (int i = 30; i > 0; i -= 4)
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{
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int b1 = p >> i & 3;
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int b2 = p >> (i - 2) & 3;
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cout << BASE[b1] << BASE[b2] << endl;
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}
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}
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// 随机生成长度为len的序列
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string generate_rand_seq(int len)
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{
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string seq(len, 'A');
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for (int i = 0; i < len; ++i)
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{
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seq[i] = BASE[rand() % 4];
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}
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return seq;
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}
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// 创建bwt矩阵
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void create_bwt_mtx(string &seq)
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{
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bwtint_t seq_len = seq.size() + 1;
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string sarr[seq_len];
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sarr[0] = seq + '$';
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for (bwtint_t i = 1; i < seq_len; ++i)
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{
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sarr[i] = sarr[0].substr(i) + sarr[0].substr(0, i);
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}
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std::sort(sarr, sarr + seq_len);
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// print bwt matrix
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// for (int i = 0; i < seq_len; ++i)
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//{
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// // cout << i << ' ' << sarr[i] << endl;
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// cout << sarr[i] << endl;
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//}
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// cout << "bwt string" << endl;
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// for (int i = 0; i < seq_len; ++i)
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// {
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// cout << sarr[i].back();
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// }
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// cout << endl;
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// cout << "pre bwt string" << endl;
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// for (int i = 0; i < seq_len; ++i)
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// {
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// cout << sarr[i][seq_len - 2];
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// }
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// cout << endl;
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}
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// 生成occ，每个字节对应一个pattern
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void fmt_gen_cnt_occ(FMTIndex *fmt)
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{
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// 0-8：大于a的occ，8-16：大于b的occ，16-24：b的occ
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int i, a, b, ti;
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uint32_t oa, ooa, ob, oob;
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for (i = 0; i != 256; ++i) // 遍历单个字节的各种情况
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{
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for (a = 0; a < 4; ++a) // ba格式
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{
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oa = 0;
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ooa = 0;
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oa += ((i >> 4 & 3) == a) + ((i & 3) == a);
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ooa += ((i >> 4 & 3) > a) + ((i & 3) > a);
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for (b = 0; b < 4; ++b)
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{
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oob = ob = 0;
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oob += ((i >> 6 & 3) > b && (i >> 4 & 3) == a) + ((i >> 2 & 3) > b && (i & 3) == a);
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ob += ((i >> 6 & 3) == b && (i >> 4 & 3) == a) + ((i >> 2 & 3) == b && (i & 3) == a);
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ti = a << 2 | b;
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fmt->cnt_occ[ti][i]= ob << 24 | oob << 16 | oa << 8 | ooa ;
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}
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}
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}
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}
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// fmt-index的count table，4对应着bwt碱基的累积量，0,1,2,3分别对应着bwt是A,C,G,T，pre-bwt的累积量
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void fmt_gen_cnt_table(uint32_t cnt_table[4][256])
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{
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int i, j, k;
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uint32_t x = 0;
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for (i = 0; i != 256; ++i) // 遍历单个字节的各种情况
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{
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for (k = 0; k < 4; ++k) // bwt碱基
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{
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x = 0; // for [A,C,G,T][A,C,G,T]
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for (j = 0; j != 4; ++j) // pre-bwt碱基
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x |= (((i >> 6 & 3) == j && (i >> 4 & 3) == k) + ((i >> 2 & 3) == j && (i & 3) == k)) << (j << 3);
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cnt_table[k][i] = x;
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}
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}
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}
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void dump_fmt(const char *fn, const FMTIndex *fmt)
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{
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FILE *fp;
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fp = xopen(fn, "wb");
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err_fwrite(&fmt->primary, sizeof(bwtint_t), 1, fp);
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err_fwrite(&fmt->sec_primary, sizeof(bwtint_t), 1, fp);
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err_fwrite(&fmt->sec_bcp, sizeof(uint8_t), 1, fp);
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err_fwrite(&fmt->first_base, sizeof(uint8_t), 1, fp);
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err_fwrite(&fmt->last_base, sizeof(uint8_t), 1, fp);
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err_fwrite(fmt->L2 + 1, sizeof(bwtint_t), 4, fp);
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err_fwrite(fmt->bwt, 4, fmt->bwt_size, fp);
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err_fflush(fp);
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err_fclose(fp);
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}
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FMTIndex *restore_fmt(const char *fn)
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{
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FMTIndex *fmt;
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fmt = (FMTIndex *)calloc(1, sizeof(FMTIndex));
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FILE *fp = fopen(fn, "rb");
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fseek(fp, 0, SEEK_END);
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fmt->bwt_size = (ftell(fp) - sizeof(bwtint_t) * 6 - 3) >> 2; // 以32位word为单位计算的size
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fmt->bwt = (uint32_t *)calloc(fmt->bwt_size, 4);
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fseek(fp, 0, SEEK_SET);
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fread(&fmt->primary, sizeof(bwtint_t), 1, fp);
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fread(&fmt->sec_primary, sizeof(bwtint_t), 1, fp);
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fread(&fmt->sec_bcp, sizeof(uint8_t), 1, fp);
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fread(&fmt->first_base, sizeof(uint8_t), 1, fp);
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fread(&fmt->last_base, sizeof(uint8_t), 1, fp);
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fread(fmt->L2 + 1, sizeof(bwtint_t), 4, fp);
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fread_fix(fp, fmt->bwt_size << 2, fmt->bwt);
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fmt->seq_len = fmt->L2[4];
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fclose(fp);
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fmt_gen_cnt_occ(fmt); // 字节所能表示的各种碱基组合中，各个碱基的累积数量
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return fmt;
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}
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// 根据interval-bwt创建fmt-index
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FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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{
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// FILE *fmt_out = fopen("fmt.txt", "w");
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FMTIndex *fmt = (FMTIndex *)calloc(1, sizeof(FMTIndex));
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fmt_gen_cnt_occ(fmt);
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bwtint_t i, j, k, m, n, n_occ, cnt[4], cnt2[4];
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uint32_t c[4], c2[16]; /*c用来保存原来的bwt碱基串的累积值，c2用来保存pre-bwt和bwt碱基对的累计值，如AA..TT*/
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uint32_t *buf; /* 计算之后变成fmt结构中bwt部分 */
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#ifdef FMT_MID_INTERVAL
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// 加入中间的check point
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uint32_t mc[4] = {0};
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uint32_t cnt_table[4][256]; // 4对应原来的cnt_table，0,1,2,3,分别对应该碱基的扩展
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fmt_gen_cnt_table(cnt_table);
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#endif
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fmt->seq_len = bwt->seq_len; // bwt碱基序列的长度，不包含$字符，也就是该长度比bwt matrix长度少1
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for (i = 0; i < 5; ++i)
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fmt->L2[i] = bwt->L2[i]; // 每个碱基的总累积值
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fmt->primary = bwt->primary; // $在末尾的行，在bwt matrix行中的排序位置
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n_occ = (bwt->seq_len + FMT_OCC_INTERVAL - 1) / FMT_OCC_INTERVAL + 1; // check point 个数
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fmt->bwt_size = (fmt->seq_len * 2 + 15) >> 4; // 要保存最后两列碱基
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fmt->bwt_size += n_occ * 20; // A,C,G,T和AA,AC.....TG,TT共20个
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#ifdef FMT_MID_INTERVAL
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bwtint_t mn_occ = (bwt->seq_len >> FMT_OCC_INTV_SHIFT) * (FMT_OCC_INTERVAL / FMT_MID_INTERVAL - 1);
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bwtint_t last_seq_len = bwt->seq_len % FMT_OCC_INTERVAL;
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mn_occ += (last_seq_len + FMT_MID_INTERVAL - 1) / FMT_MID_INTERVAL - 1;
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fmt->bwt_size += mn_occ * 4;
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//cout << "mn_occ: " << mn_occ << endl;
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//exit(0);
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#endif
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buf = (uint32_t *)calloc(fmt->bwt_size, 4); // 开辟计算fmt用到的缓存
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c[0] = c[1] = c[2] = c[3] = 0;
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// 首行的c2，应该是对应的ACGT对应的行，减去1的occ
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for (i = 0; i < 4; ++i)
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{
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bwtint_t before_first_line = fmt->L2[i];
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bwt_occ4(bwt, before_first_line, cnt);
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for (j = i * 4, k = 0; k < 4; ++j, ++k)
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c2[j] = cnt[k];
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}
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// k表示buf存储的偏移量
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for (i = k = 0; i < bwt->seq_len; ++i)
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{
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// 记录occ
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if (i % FMT_OCC_INTERVAL == 0)
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{
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memcpy(buf + k, c, sizeof(uint32_t) * 4); // bwt str中各个碱基的occ
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k += 4;
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memcpy(buf + k, c2, sizeof(uint32_t) * 16); // pre-bwt:bwt碱基对的occ
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k += 16;
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#ifdef FMT_MID_INTERVAL
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mc[0] = mc[1] = mc[2] = mc[3] = 0;
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#endif
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}
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// 每个32位整数保存8个倒数第二列碱基（pre-bwt）和8个倒数第一列(bwt)碱基
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if (i % 16 == 0) // 每个32位整数可以包含16个碱基，每次需要处理16个碱基，也就是间隔最小可以设置为16
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{
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uint32_t pre_bwt_16_seq = 0; // 16个pre-bwt碱基串
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uint32_t *bwt_addr = bwt_occ_intv(bwt, i) + 4; // 这里加4还是加8要看保存occ的是是uint32还是uint64，bwt字符串i对应的基准行，因为原始的bwt-cp（check point）包含由4个uint32_t(8个uint32_t)组成的occ信息
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int offset = (i % OCC_INTERVAL) / 16; // 每OCC_INTERVAL个碱基共享同一个基准地址，每16个碱基共用一个uint32整型，因此需要偏移量来获取当前碱基串的首地址
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uint32_t bwt_16_seq = *(bwt_addr + offset); // 待处理的当前16个碱基串的首地址
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for (j = 0; j < 16; ++j) // 对于bwt碱基串，一个一个碱基分别处理
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{
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bwtint_t cur_str_line = i + j; // 当前碱基在bwt str中的行排序
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if (cur_str_line < bwt->seq_len) // 当前碱基行不应超出bwt str总碱基长度（bwt str长度比bwt matrix长度少1，因为bwt str不包含$）
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{
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uint8_t bwt_base = bwt_B0(bwt, cur_str_line); // 对应行的bwt的碱基
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// 先求出该碱基对应在第一列的行（对应的bwt matrix行）
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bwtint_t cur_mtx_line = cur_str_line;
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if (cur_str_line >= bwt->primary) // 因为bwt序列里除去了$符号，所以，超过$所在行之后，对应的seq位置应该加一，才是真正对应bwt matrix的行
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cur_mtx_line += 1;
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bwt_occ4(bwt, cur_mtx_line, cnt); // 获取原来bwt-checkpoint中的occ值
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for (m=0; m<4; ++m)
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c[m] = (uint32_t)cnt[m]; // 碱基m在cur_bwt_mtx_line(包含)之前的累积值，直接拷贝原bwt中的occ即可
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cnt[bwt_base] -= 1; // 得到cur_bwt_mtx_line(不包含)之前的累积量，即bwt_occ4(bwt, cur_bwt_mtx_line-1, cnt)
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bwtint_t bwt_base_mtx_line = bwt->L2[bwt_base] + 1 + cnt[bwt_base]; // bwt_base对应的bwt matrix行（LF变换）
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bwt_occ4(bwt, bwt_base_mtx_line, cnt2); // 计算bwt_base_mtx_line之前的occ
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for (n = 0; n < 4; ++n)
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{
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int c2_idx = bwt_base << 2 | n; // bwt base放在前边
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c2[c2_idx] = (uint32_t)cnt2[n]; // pre-bwt:bwt 碱基对的累计值
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}
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bwtint_t bwt_base_str_line = bwt_base_mtx_line; // bwt-str中对应的行排序
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if (bwt_base_str_line >= bwt->primary) // base_line表示在bwt str中的位置，所以超出$为最尾所在行之后，要减掉1
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bwt_base_str_line -= 1; // bwt碱基序列行（不包含$）
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uint32_t pre_bwt_base = bwt_B0(bwt, bwt_base_str_line); // bwt列碱基对应的前一个碱基pre-bwt
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// 此时，bwt_base对应的bwt matrix首行，是$排在最尾的行，说明bwt_base就是序列的第一个碱基，
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// 此时计算出来的pre_bwt_base就是primary前一行的bwt base，以此来代替$字符，在后续的计算过程中需要考虑
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if (bwt_base_mtx_line == bwt->primary)
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{
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// 计算sec_bcp
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fmt->sec_bcp = pre_bwt_base << 2 | bwt_base; // 因为把$当成A处理了
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fmt->sec_primary = cur_mtx_line; // pre-bwt base为$的行排序（bwt-matrix行）
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fmt->first_base = bwt_base; // 原始序列第一个碱基
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fmt->last_base = pre_bwt_base; // 计算后替代$字符的碱基（应该是primary行上边一行对应的bwt base）
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}
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// 暂存 pre-bwt碱基序列
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pre_bwt_16_seq = pre_bwt_16_seq | (pre_bwt_base << (15-j)*2); // 序列靠前的碱基排在uint32_t数据中的高位
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// 输出调试信息
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// cout << "mtx line: " << cur_mtx_line << ' ' << c[0] << ' ' << c[1] << ' ' << c[2] << ' ' << c[3] << ' ';
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// for (m = 0; m < 16; ++m)
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// cout << c2[m] << ' ';
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// cout << endl;
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}
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else
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break;
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}
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// 保存bwt和pre_bwt
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uint32_t pre_and_bwt_seq = 0;
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uint32_t pre_and_bwt_seq_2 = 0;
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for (m = 0; m < 8; ++m)
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{
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int lshift_bit = 30 - 2 * m;
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pre_and_bwt_seq |= (((pre_bwt_16_seq & (3 << lshift_bit)) >> (m * 2)) | ((bwt_16_seq & (3 << lshift_bit)) >> ((m * 2) + 2)));
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}
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buf[k++] = pre_and_bwt_seq;
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if (j > 8)
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{
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#if FMT_MID_INTERVAL == 8
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for (m = 0; m < 4; ++m)
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{
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uint32_t s1 = pre_and_bwt_seq;
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mc[m] += cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24];
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buf[k++] = mc[m];
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}
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#endif
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for (m = 8; m > 0; --m)
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{
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int lshift_bit = 2 * m - 2;
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pre_and_bwt_seq_2 |= (((pre_bwt_16_seq & (3 << lshift_bit)) << (m * 2)) | ((bwt_16_seq & (3 << lshift_bit)) << (m * 2 - 2)));
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}
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buf[k++] = pre_and_bwt_seq_2;
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#if FMT_MID_INTERVAL == 8
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if ((i + 16) % FMT_OCC_INTERVAL != 0 && j == 16)
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for (m = 0; m < 4; ++m)
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{
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uint32_t s1 = pre_and_bwt_seq_2;
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mc[m] += cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24];
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buf[k++] = mc[m];
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}
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#endif
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}
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#if FMT_MID_INTERVAL == 16
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// 加入中间的check point
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for (m = 0; m < 4; ++m)
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{
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uint32_t s1 = pre_and_bwt_seq;
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mc[m] += cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24];
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s1 = pre_and_bwt_seq_2;
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mc[m] += cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24];
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}
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if ((i + 16) % FMT_OCC_INTERVAL != 0 && j > 8) // 序列最后的部分不用保存
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{
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for (m = 0; m < 4; ++m)
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buf[k++] = mc[m];
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}
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#endif
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}
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}
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// the last element
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memcpy(buf + k, c, sizeof(uint32_t) * 4);
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k += 4;
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memcpy(buf + k, c2, sizeof(uint32_t) * 16);
|
||
k += 16;
|
||
// cout << "n occ: " << n_occ << endl;
|
||
cout << "size: " << k << '\t' << fmt->bwt_size << endl;
|
||
xassert(k == fmt->bwt_size, "inconsistent bwt_size");
|
||
// update fmt
|
||
fmt->bwt = buf;
|
||
return fmt;
|
||
}
|
||
|
||
// 扩展两个个碱基，计算bwt base为b的pre-bwt str中各个碱基的occ
|
||
void fmt_e2_occ(const FMTIndex *fmt, bwtint_t k, int b1, int b2, bwtint_t cnt[4])
|
||
{
|
||
uint32_t x = 0;
|
||
uint32_t *p, *q, tmp;
|
||
bwtint_t bwt_k_line = k, bwt_k_base_line = k >> FMT_OCC_INTV_SHIFT << FMT_OCC_INTV_SHIFT;
|
||
int i, ti;
|
||
cnt[0] = 0;
|
||
cnt[1] = 0;
|
||
cnt[2] = 0;
|
||
if (k == (bwtint_t)(-1))
|
||
{
|
||
p = fmt->bwt + 4 + b1 * 4;
|
||
for (i = b2 + 1; i < 4; ++i) cnt[2] += p[i];
|
||
cnt[3] = p[b2];
|
||
return;
|
||
}
|
||
ti = b1 << 2 | b2;
|
||
k -= (k >= fmt->primary); // k由bwt矩阵对应的行转换成bwt字符串对应的行（去掉了$，所以大于$的行，都减掉1）
|
||
p = fmt_occ_intv(fmt, k);
|
||
//cout << "k-base: " << k << "; occ: " << p[0] << ' ' << p[1] << ' ' << p[2] << ' ' << p[3] << endl;
|
||
for (i = b1 + 1; i < 4; ++i) cnt[0] += p[i]; // 大于b1的碱基的occ之和
|
||
cnt[1] = p[b1]; // b1的occ
|
||
q = p + 4 + b1 * 4;
|
||
for (i = b2 + 1; i < 4 ; ++i) cnt[2] += q[i]; // 大于b2的occ之和
|
||
cnt[3] = q[b2]; // b2的occ
|
||
p += 20;
|
||
|
||
//if (k == 3965453116 || k == 3965453672 || k == 2668688087 || k == 2668688550) {
|
||
// cout << "sec base-occ: " << q[0] << ' ' << q[1] << ' ' << q[2] << ' ' << q[3] << endl;
|
||
//}
|
||
#ifdef FMT_MID_INTERVAL
|
||
// 使用mid interval信息
|
||
int mk = k % FMT_OCC_INTERVAL;
|
||
int n_mintv = mk >> FMT_MID_INTV_SHIFT;
|
||
//if (k == 3137454504)
|
||
//{
|
||
// for (i = 0; i < n_mintv; ++i)
|
||
// {
|
||
// q = p + i * 6;
|
||
// print_base_uint32(*q);
|
||
// print_base_uint32(*(q + 1));
|
||
// x = *(q + 2);
|
||
// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
|
||
// x = *(q + 3);
|
||
// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
|
||
// x = *(q + 4);
|
||
// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
|
||
// x = *(q + 5);
|
||
// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
|
||
// }
|
||
// x = 0;
|
||
//}
|
||
if (n_mintv > 0) // 至少超过了第一个mid interval
|
||
{
|
||
p += n_mintv * (4 + (FMT_MID_INTERVAL >> 3)) - 4; // 对应的mid interval check point的首地址，即A C G T的局部累积量
|
||
q = p + b1;
|
||
for (i = b1 + 1; i < 4; ++i)
|
||
x += p[i]; // 大于b1的碱基的occ之和
|
||
cnt[0] += __fmt_mid_sum(x);
|
||
x = *q;
|
||
// if (k == 3137454504)
|
||
// {
|
||
// cout << ((x) >> 24 & 0xff) << '\t' << ((x) >> 16 & 0xff)
|
||
// << '\t' << ((x) >> 8 & 0xff) << '\t' << ((x) & 0xff) << endl;
|
||
// cout << __fmt_mid_sum(x) << endl;
|
||
// }
|
||
cnt[1] += __fmt_mid_sum(x); // b1的occ
|
||
for (i = 3; i > b2; --i)
|
||
cnt[2] += x >> (i << 3) & 0xff; // 大于b2的occ之和
|
||
cnt[3] += x >> (b2 << 3) & 0xff; // b2的occ
|
||
x = 0;
|
||
p += 4;
|
||
}
|
||
// cout << "mid-occ: " << cnt[0] << ' ' << cnt[1] << ' ' << cnt[2] << ' ' << cnt[3] << endl;
|
||
// cout << "k: " << k << ' ' << cnt[1] << endl;
|
||
#if FMT_MID_INTERVAL == 16
|
||
if ((mk & FMT_MID_INTV_MASK) >> 3)
|
||
{
|
||
x += __fmt_occ_e2_aux2(fmt, ti, *p);
|
||
// print_base_uint32(*p);
|
||
++p;
|
||
}
|
||
#endif
|
||
tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
|
||
x += __fmt_occ_e2_aux2(fmt, ti, tmp);
|
||
//if (k == 3965453116 || k == 3965453672 || k == 2668688087 || k == 2668688550)
|
||
//{
|
||
// print_base_uint32(tmp);
|
||
// cout << "多的: " << (~k & 7) << endl;
|
||
// cout << (x >> 24 & 0xff) << ' ' << (x >> 16 & 0xff) << ' ' << (x >> 8 & 0xff) << ' ' << (x & 0xff) << endl;
|
||
//}
|
||
#else // 该地址是bwt和pre_bwt字符串数据的首地址
|
||
uint32_t *end = p + ((k >> 3) - ((k & ~FMT_OCC_INTV_MASK) >> 3)); // this is the end point of the following loop
|
||
// p = end - (end - p) / 8;
|
||
// cout << "k - kbase: " << k - bwt_k_base_line << endl;
|
||
for (; p < end; ++p)
|
||
{
|
||
x += __fmt_occ_e2_aux2(fmt, ti, *p);
|
||
// print_base_uint32(*p);
|
||
}
|
||
tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
|
||
// print_base_uint32(tmp);
|
||
x += __fmt_occ_e2_aux2(fmt, ti, tmp);
|
||
#endif
|
||
|
||
if (b1 == 0)
|
||
{
|
||
x -= (~k & 7) << 8;
|
||
if (b2 == 0)
|
||
x -= (~k & 7) << 24;
|
||
// cout << "here-1" << endl;
|
||
}
|
||
// 如果跨过了second_primary,那么可能需要减掉一次累积值
|
||
if (b1 == fmt->first_base && bwt_k_base_line < fmt->sec_primary && bwt_k_line >= fmt->sec_primary)
|
||
{
|
||
if (b2 < fmt->last_base)
|
||
cnt[2] -= 1 ;
|
||
else if (b2 == fmt->last_base)
|
||
cnt[3] -= 1;
|
||
// cout << "here-2" << endl;
|
||
|
||
}
|
||
// if (k == 3965453116 || k == 3965453672 || k == 2668688087 || k == 2668688550)
|
||
// {
|
||
// cout << BASE[b1] << BASE[b2] << endl;
|
||
// cout << "final-x: " << (x >> 24 & 0xff) << ' ' << (x >> 16 & 0xff) << ' ' << (x >> 8 & 0xff) << ' ' << (x & 0xff) << endl;
|
||
// }
|
||
|
||
cnt[0] += x & 0xff;
|
||
cnt[1] += x >> 8 & 0xff;
|
||
cnt[2] += x >> 16 & 0xff;
|
||
cnt[3] += x >> 24 & 0xff;
|
||
// if (k == 3965453116 || k == 3965453672 || k == 2668688087 || k == 2668688550)
|
||
// cout << "final-occ: " << cnt[0] << ' ' << cnt[1] << ' ' << cnt[2] << ' ' << cnt[3] << endl;
|
||
}
|
||
|
||
// 扩展两个碱基
|
||
void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok, int is_back, int b1, int b2)
|
||
{
|
||
bwtint_t tk[4], tl[4], first_pos;
|
||
// tk表示在k行之前所有各个碱基累积出现次数，tl表示在l行之前的累积
|
||
fmt_e2_occ(fmt, ik->x[!is_back] - 1, b1, b2, tk);
|
||
fmt_e2_occ(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tl);
|
||
//fmt_e2_occ_2way(fmt, ik->x[!is_back] - 1, b1, b2, tk);
|
||
//fmt_e2_occ_2way(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tl);
|
||
// 这里是反向扩展
|
||
//cout << BASE[b1] << BASE[b2] << endl;
|
||
//cout << "fmt: interval-1: " << tl[0] - tk[0] << ' ' << tl[0] << ' ' << tk[0] << endl;
|
||
//cout << "fmt: interval-2: " << tl[2] - tk[2] << ' ' << tl[2] << ' ' << tk[2] << endl;
|
||
ok->x[!is_back] = fmt->L2[b2] + 1 + tk[3];
|
||
ok->x[2] = tl[3] - tk[3];
|
||
// 第一次正向扩展
|
||
ok->x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= fmt->primary && ik->x[!is_back] + ik->x[2] - 1 >= fmt->primary) + tl[0] - tk[0];
|
||
// 第二次正向扩展
|
||
first_pos = fmt->L2[b1] + 1 + tk[1];
|
||
ok->x[is_back] = ok->x[is_back] + (first_pos <= fmt->primary && first_pos + tl[1] - tk[1] - 1 >= fmt->primary) + tl[2] - tk[2];
|
||
}
|
||
|
||
// 扩展一个碱基
|
||
void fmt_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok, int is_back, int b1)
|
||
{
|
||
bwtint_t tk[4], tl[4];
|
||
int b2 = 3;
|
||
// tk表示在k行之前所有各个碱基累积出现次数，tl表示在l行之前的累积
|
||
fmt_e2_occ(fmt, ik->x[!is_back] - 1, b1, b2, tk);
|
||
fmt_e2_occ(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tl);
|
||
//fmt_e2_occ_2way(fmt, ik->x[!is_back] - 1, b1, b2, tk);
|
||
//fmt_e2_occ_2way(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tl);
|
||
// 这里是反向扩展
|
||
ok->x[!is_back] = fmt->L2[b1] + 1 + tk[1];
|
||
ok->x[2] = tl[1] - tk[1];
|
||
// 第一次正向扩展
|
||
ok->x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= fmt->primary && ik->x[!is_back] + ik->x[2] - 1 >= fmt->primary) + tl[0] - tk[0];
|
||
}
|
||
|
||
// 利用fmt搜索seed，完整搜索，只需要单向搜索
|
||
bwtintv_t fmt_search(FMTIndex *fmt, const string &q)
|
||
{
|
||
bwtintv_t ik;
|
||
bwtintv_t ok;
|
||
int i, c1, c2, x = 0;
|
||
int qlen = (int)q.size();
|
||
|
||
fmt_set_intv(fmt, bval(q[x]), ik);
|
||
ik.info = x + 1;
|
||
//cout << "fmt : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
|
||
|
||
for (i = x + 1; i + 1 < qlen; i += 2)
|
||
{
|
||
if (bval(q[i]) < 4 && bval(q[i + 1]) < 4)
|
||
{
|
||
c1 = cbval(q[i]);
|
||
c2 = cbval(q[i + 1]);
|
||
//cout << BASE[c2] << BASE[c1] << endl;
|
||
//double tm_t = realtime();
|
||
fmt_extend2(fmt, &ik, &ok, 0, c1, c2);
|
||
ik = ok;
|
||
// t8 += realtime() - tm_t;
|
||
ik.info = i + 1;
|
||
//cout << "fmt : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
|
||
}
|
||
else
|
||
{
|
||
break;
|
||
}
|
||
}
|
||
if (i < qlen && bval(q[i]) < 4)
|
||
{ // 最后一次扩展
|
||
c1 = cbval(q[i]);
|
||
// double tm_t = realtime();
|
||
fmt_extend1(fmt, &ik, &ok, 0, c1);
|
||
ik = ok;
|
||
// t9 += realtime() - tm_t;
|
||
ik.info = i + 1;
|
||
//cout << "fmt : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
|
||
}
|
||
// cout << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
|
||
return ik;
|
||
}
|
||
|
||
uint32_t str2bit(string &str)
|
||
{
|
||
uint32_t pac = 0;
|
||
for (int i = 0; i < 16; ++i)
|
||
pac = (pac << 2) | bval(str[i]);
|
||
return pac;
|
||
}
|
||
|
||
int main_fmtidx(int argc, char **argv)
|
||
{
|
||
// string seq("ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA");
|
||
string seq("ACCCT");
|
||
string rseq = calc_reverse_seq(seq);
|
||
seq = seq + rseq;
|
||
//create_bwt_mtx(seq);
|
||
//cout << seq << endl;
|
||
|
||
// uint32_t cnt_table[4][256];
|
||
// fmt_gen_cnt_table(cnt_table);
|
||
// string ss1("ATATATCAATTCTCTT");
|
||
// string ss2("ATTGCCTCTGAATTAC");
|
||
// uint32_t bs1 = str2bit(ss1), bs2 = str2bit(ss2);
|
||
// uint32_t s1 = bs1;
|
||
// uint32_t x = 0;
|
||
// for (int m = 0; m < 4; ++m)
|
||
// {
|
||
// x = cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24];
|
||
// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
|
||
// }
|
||
// x = 0;
|
||
// s1 = bs2;
|
||
// for (int m = 0; m < 4; ++m)
|
||
// {
|
||
// x = cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24];
|
||
// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
|
||
// }
|
||
|
||
// return 0;
|
||
|
||
// string bwt_str = string(argv[1]) + ".bwt.str";
|
||
string bwt_idx = string(argv[1]) + ".128.bwt";
|
||
// string bwt_idx = string(argv[1]) + ".64.bwt";
|
||
// string bwt_idx = string(argv[1]) + ".16.bwt";
|
||
// string bwt_idx = string(argv[1]) + ".bwt";
|
||
//bwt_t *bwt = restore_bwt(bwt_str.c_str());
|
||
//create_interval_occ_bwt(bwt);
|
||
//dump_bwt(bwt_idx.c_str(), bwt);
|
||
|
||
//string fmt_idx = string(argv[1]) + ".fmt";
|
||
//string fmt_idx = string(argv[1]) + ".256.8.fmt";
|
||
string fmt_idx = string(argv[1]) + ".256.fmt";
|
||
//string fmt_idx = string(argv[1]) + ".128.fmt";
|
||
// string fmt_idx = string(argv[1]) + ".64.fmt";
|
||
// string fmt_idx = string(argv[1]) + ".32.fmt";
|
||
|
||
t11 = realtime();
|
||
bwt_t *bwt = restore_bwt(bwt_idx.c_str());
|
||
t11 = realtime() - t11;
|
||
cout << "[time read bwt:] " << t11 << "s" << endl;
|
||
t10 = realtime();
|
||
FMTIndex *fmt = restore_fmt(fmt_idx.c_str());
|
||
//FMTIndex *fmt = create_fmt_from_bwt(bwt);
|
||
//dump_fmt(fmt_idx.c_str(), fmt);
|
||
t10 = realtime() - t10;
|
||
cout << "[time gen fmt:] " << t10 << "s" << endl;
|
||
|
||
vector<string> seed_arr(10000000);
|
||
seed_arr[0] = "GCGATACTAAGA";
|
||
seed_arr[0] = "GAGAGCTGTTCCCGTGTTTTCCATGGTTT";
|
||
srand(time(NULL));
|
||
|
||
t1 = realtime();
|
||
for (int i = 0; i < (int)seed_arr.size(); ++i)
|
||
seed_arr[i] = generate_rand_seq(7);
|
||
t1 = realtime() - t1;
|
||
cout << "[time gen seed:] " << t1 << "s" << endl;
|
||
|
||
t2 = realtime();
|
||
for (int i = 0; i < (int)seed_arr.size(); ++i)
|
||
bwt_search(bwt, seed_arr[i]);
|
||
t2 = realtime() - t2;
|
||
cout << "[time bwt search:] " << t2 << "s" << endl;
|
||
t3 = realtime();
|
||
for (int i = 0; i < (int)seed_arr.size(); ++i)
|
||
fmt_search(fmt, seed_arr[i]);
|
||
t3 = realtime() - t3;
|
||
cout << "[time fmt search:] " << t3 << "s" << endl;
|
||
|
||
//return 0;
|
||
|
||
t4 = realtime();
|
||
for (int i = 0; i < (int)seed_arr.size(); ++i)
|
||
{
|
||
bwtintv_t p1 =
|
||
bwt_search2(bwt, seed_arr[i]);
|
||
bwtintv_t p2 = fmt_search(fmt, seed_arr[i]);
|
||
if (p1.x[0] != p2.x[0] || p1.x[1] != p2.x[1] || p1.x[2] != p2.x[2])
|
||
cout << seed_arr[i] << endl
|
||
<< p1.x[0] << ' ' << p1.x[1] << ' ' << p1.x[2] << endl
|
||
<< p2.x[0] << ' ' << p2.x[1] << ' ' << p2.x[2] << endl;
|
||
}
|
||
t4 = realtime() - t4;
|
||
cout << "[time bwt search 2:] " << t4 << "s" << endl;
|
||
|
||
//cout << "bwt occ: " << t5 << "s; " << t7 << '\t' << t10 << endl;
|
||
//cout << "fmt occ: " << t6 << "s; " << t11 << '\t' << t8 << '\t' << t9 << endl;
|
||
// bwt_search(bwt, s);
|
||
// bwt_search2(bwt, s);
|
||
// for (int i = 0; i < 120; ++i)
|
||
// {
|
||
// cout << i << '\t' << bwt_B0(bwt, i) << endl;
|
||
// }
|
||
// TGGGAT
|
||
// FMTIndex *fmt = create_fmt_from_bwt(bwt);
|
||
// dump_fmt("ref.fmt", fmt);
|
||
// FMTIndex *fmt = restore_fmt("tiny.fmt");
|
||
|
||
//fmt_search(fmt, s);
|
||
// cout << bwt->bwt_size << endl;
|
||
// cout << bwt->seq_len << endl;
|
||
//cout << "sec_: " << fmt->sec_bcp << '\t' << fmt->sec_primary << endl;
|
||
|
||
//uint8_t b8 = 2 << 4 | 2;
|
||
//cout << "AGAG: " << fmt->cnt_table[2][b8] << endl;
|
||
//cout << (((b8 >> 6) == 0 && (b8 >> 4 & 3) == 2) + ((b8 >> 2 & 3) == 0 && (b8 & 3) == 2)) << endl;
|
||
return 0;
|
||
} |