mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
807 lines
14 KiB
C++
807 lines
14 KiB
C++
#include "Levenshtein_distance.h"
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void output_bit_myers(Word x, int length)
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{
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int i = 0;
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while (i < length)
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{
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fprintf(stderr, "%u", (x >> i) & ((Word)1));
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i++;
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}
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fprintf(stderr, "\n");
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}
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void prase_vertical(Word VP, Word VN, int length, int matrix[1000][1000], int i)
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{
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i++;
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int k = 0;
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int j = i;
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int diff;
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while (k < length)
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{
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int x_p = (VP >> k) & ((Word)1);
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int x_n = (VN >> k) & ((Word)1);
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if (x_p == 1 && x_n == 1)
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{
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fprintf(stderr, "error\n");
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}
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if (x_p == 1)
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{
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diff = 1;
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///fprintf(stderr, "[+1]");
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}
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if (x_n == 1)
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{
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diff = -1;
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///fprintf(stderr, "[-1]");
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}
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if (x_p == 0 && x_n == 0)
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{
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diff = 0;
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///fprintf(stderr, "[+0]");
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}
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j++;
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if (matrix[i][j] - matrix[i][j - 1] != diff)
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{
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fprintf(stderr, "*************V(k): %u\n", k);
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///return;
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}
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k++;
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}
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///fprintf(stderr, "\n");
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}
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void prase_D0(Word D0, int length, int matrix[1000][1000], int i)
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{
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i++;
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int k = 0;
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int j = i;
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int diff;
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while (k < length)
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{
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int diff = (D0 >> k) & ((Word)1);
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if(diff==matrix[i][j] - matrix[i-1][j-1])
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{
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fprintf(stderr, "*************D(k): %u\n", k);
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fprintf(stderr, "diff: %u, matrix[i][j]: %u, matrix[i-1][j-1]: %u\n", diff, matrix[i][j], matrix[i-1][j-1]);
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///return;
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}
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j++;
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k++;
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}
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///fprintf(stderr, "\n");
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}
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void prase_H(Word HP, Word HN, int length, int matrix[1000][1000], int i)
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{
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i++;
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int k = 0;
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int j = i;
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int diff;
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while (k < length)
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{
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int x_p = (HP >> k) & ((Word)1);
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int x_n = (HN >> k) & ((Word)1);
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if (x_p == 1 && x_n == 1)
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{
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fprintf(stderr, "error\n");
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}
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if (x_p == 1)
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{
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diff = 1;
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///fprintf(stderr, "[+1]");
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}
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if (x_n == 1)
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{
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diff = -1;
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///fprintf(stderr, "[-1]");
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}
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if (x_p == 0 && x_n == 0)
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{
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diff = 0;
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///fprintf(stderr, "[+0]");
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}
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if(diff!=matrix[i][j] - matrix[i-1][j])
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{
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fprintf(stderr, "*************H(k): %u\n", k);
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///return;
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}
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j++;
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k++;
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}
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///fprintf(stderr, "\n");
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}
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/**
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pattern是长的那个，是y
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p_length是长的那个的长度, p_length实际没用
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text是短的那个，是x
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t_length是短的那个的长度
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errthold是阈值
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return_err是编辑距离
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返回值是结束位置
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**/
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int Reserve_Banded_BPM_debug
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(char *pattern, int p_length, char *text, int t_length, unsigned short errthold, unsigned int* return_err, int matrix[1000][1000])
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{
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(*return_err) = (unsigned int)-1;
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Word Peq[256];
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int band_length = (errthold << 1) + 1;
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int i = 0;
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Word tmp_Peq_1 = (Word)1;
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Peq['A'] = (Word)0;
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Peq['T'] = (Word)0;
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Peq['G'] = (Word)0;
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Peq['C'] = (Word)0;
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Word Peq_A;
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Word Peq_T;
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Word Peq_C;
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Word Peq_G;
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///band_length = 2k + 1
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for (i = 0; i<band_length; i++)
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{
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Peq[pattern[i]] = Peq[pattern[i]] | tmp_Peq_1;
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tmp_Peq_1 = tmp_Peq_1 << 1;
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}
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///Peq['T'] = Peq['T'] | Peq['C'];
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Peq_A = Peq['A'];
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Peq_C = Peq['C'];
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Peq_T = Peq['T'];
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Peq_G = Peq['G'];
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memset(Peq, 0, sizeof(Word)* 256);
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Peq['A'] = Peq_A;
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Peq['C'] = Peq_C;
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Peq['T'] = Peq_T;
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Peq['G'] = Peq_G;
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Word Mask = ((Word)1 << (errthold << 1));
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Word VP = 0;
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Word VN = 0;
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Word X = 0;
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Word D0 = 0;
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Word HN = 0;
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Word HP = 0;
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i = 0;
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int err = 0;
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Word err_mask = (Word)1;
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///band_down = 2k
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///i_bd = 2k
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///int i_bd = i + band_down;
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int i_bd = (errthold << 1);
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int last_high = (errthold << 1);
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/// t_length_1 = SEQ_LENGTH - 1
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int t_length_1 = t_length - 1;
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//while(i<t_length)
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while (i<t_length_1)
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{
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fprintf(stderr, "i: %u, j_s: %u, j_e: %u\n", i + 1, i + 1, i + band_length + 1);
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///if (i >= 6)
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if (i >= 0)
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{
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/**
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fprintf(stderr, "VP:\n");
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output_bit_myers(VP, band_length);
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fprintf(stderr, "VN:\n");
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output_bit_myers(VN, band_length);
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fprintf(stderr, "HP:\n");
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output_bit_myers(HP, band_length);
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fprintf(stderr, "HN:\n");
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output_bit_myers(HN, band_length);
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fprintf(stderr, "D0:\n");
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output_bit_myers(D0, band_length);
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fprintf(stderr, "text[i]: %c\n", text[i]);
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fprintf(stderr, "Peq[text[i]]:\n");
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output_bit_myers(Peq[text[i]], band_length);
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for (size_t j = i; j < i + band_length; j++)
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{
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fprintf(stderr, "%c", pattern[j]);
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}
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fprintf(stderr, "\n");
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fprintf(stderr, "Previous begin.\n");
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prase_vertical(VP, VN, band_length, matrix, i-1);
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prase_D0(D0, band_length, matrix, i-1);
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prase_H(HP, HN, band_length, matrix, i-1);
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fprintf(stderr, "Previous test done.\n");
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**/
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X = Peq[text[i]] | VN;
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/**
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fprintf(stderr, "#X:\n");
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output_bit_myers(X, band_length);
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**/
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D0 = ((VP + (X&VP)) ^ VP) | X;
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/**
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fprintf(stderr, "#(X&VP):\n");
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output_bit_myers((X&VP), band_length);
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fprintf(stderr, "#(VP + (X&VP)):\n");
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output_bit_myers((VP + (X&VP)), band_length);
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fprintf(stderr, "#((VP + (X&VP)) ^ VP):\n");
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output_bit_myers(((VP + (X&VP)) ^ VP), band_length);
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fprintf(stderr, "#D0:\n");
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output_bit_myers(D0, band_length);
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**/
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HN = VP&D0;
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HP = VN | ~(VP | D0);
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X = D0 >> 1;
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VN = X&HP;
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VP = HN | ~(X | HP);
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}
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else
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{
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///pattern[0]ÔÚPeq[2k], ¶øpattern[2k]ÔÚPeq[0]
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X = Peq[text[i]] | VN;
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D0 = ((VP + (X&VP)) ^ VP) | X;
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HN = VP&D0;
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HP = VN | ~(VP | D0);
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X = D0 >> 1;
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VN = X&HP;
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VP = HN | ~(X | HP);
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}
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/**
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for (size_t j = i + 1; j <= i + band_length + 1; j++)
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{
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fprintf(stderr, "[%u]", matrix[i + 1][j]);
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}
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fprintf(stderr, "\n");
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**/
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prase_vertical(VP, VN, band_length, matrix, i);
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prase_D0(D0, band_length, matrix, i);
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prase_H(HP, HN, band_length, matrix, i);
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/**
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fprintf(stderr, "VP:\n");
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output_bit_myers(VP, band_length);
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fprintf(stderr, "VN:\n");
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output_bit_myers(VN, band_length);
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**/
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if (!(D0&err_mask))
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{
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++err;
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///¼´Ê¹È«²¿µÝ¼õ£¬Ò²¾Í¼õ2k
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if ((err - last_high)>errthold)
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{
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///fprintf(stderr, "0 ######, i: %u\n", i);
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return -1;
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}
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}
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Peq['A'] = Peq['A'] >> 1;
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Peq['C'] = Peq['C'] >> 1;
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Peq['G'] = Peq['G'] >> 1;
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Peq['T'] = Peq['T'] >> 1;
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++i;
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++i_bd;
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Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
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///Peq['T'] = Peq['T'] | Peq['C'];
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}
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X = Peq[text[i]] | VN;
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D0 = ((VP + (X&VP)) ^ VP) | X;
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HN = VP&D0;
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HP = VN | ~(VP | D0);
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X = D0 >> 1;
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VN = X&HP;
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VP = HN | ~(X | HP);
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if (!(D0&err_mask))
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{
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++err;
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if ((err - last_high)>errthold)
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return -1;
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}
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prase_vertical(VP, VN, band_length, matrix, i);
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prase_D0(D0, band_length, matrix, i);
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prase_H(HP, HN, band_length, matrix, i);
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fprintf(stderr, "err: %d, matrix[][]: %d\n", err, matrix[i+1][i+1]);
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fprintf(stderr, "VP:\n");
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output_bit_myers(VP, band_length);
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fprintf(stderr, "VN:\n");
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output_bit_myers(VN, band_length);
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////fprintf(stderr, "sucess(2)\n");
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/// last_high = 2k
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/// site = (SEQ_LENGTH + 2k) - 2k -1
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/// site = SEQ_LENGTH - 1
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///int site = p_length - last_high - 1;
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int site = t_length - 1;
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int return_site = -1;
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if ((err <= errthold) && (err<=*return_err))
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{
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*return_err = err;
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return_site = site;
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}
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int i_last = i;
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i = 0;
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while (i<errthold)
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{
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err = err + ((VP >> i)&(Word)1);
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err = err - ((VN >> i)&(Word)1);
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++i;
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fprintf(stderr, "*i: %u, err: %d\n", i, err);
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if ((err <= errthold) && (err <= *return_err))
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{
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*return_err = err;
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return_site = site + i;
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}
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}
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unsigned int ungap_err;
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ungap_err = err;
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while (i<last_high)
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{
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err = err + ((VP >> i)&(Word)1);
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err = err - ((VN >> i)&(Word)1);
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++i;
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fprintf(stderr, "*i: %u, err: %d\n", i, err);
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if ((err <= errthold) && (err<=*return_err))
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{
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*return_err = err;
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return_site = site + i;
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}
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}
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if ((ungap_err <= errthold) && (ungap_err == *return_err))
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{
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return_site = site + errthold;
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}
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return return_site;
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}
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int BS_Reserve_Banded_BPM
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(char *pattern, int p_length, char *text, int t_length, unsigned short errthold, unsigned int* return_err)
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{
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(*return_err) = (unsigned int)-1;
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///Õâ¸öÊÇÄǸöÐèÒªÔ¤´¦ÀíµÄÏòÁ¿
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Word Peq[256];
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int band_length = (errthold << 1) + 1;
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int i = 0;
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Word tmp_Peq_1 = (Word)1;
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Peq['A'] = (Word)0;
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Peq['T'] = (Word)0;
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Peq['G'] = (Word)0;
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Peq['C'] = (Word)0;
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Word Peq_A;
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Word Peq_T;
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Word Peq_C;
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Word Peq_G;
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///band_length = 2k + 1
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///ÕâÊÇ°ÑpatternµÄÇ°2k + 1¸ö×Ö·ûÔ¤´¦Àí
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///pattern[0]¶ÔÓ¦Peq[0]
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///pattern[2k]¶ÔÓ¦Peq[2k]
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for (i = 0; i<band_length; i++)
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{
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Peq[pattern[i]] = Peq[pattern[i]] | tmp_Peq_1;
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tmp_Peq_1 = tmp_Peq_1 << 1;
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}
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Peq['T'] = Peq['T'] | Peq['C'];
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Peq_A = Peq['A'];
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Peq_C = Peq['C'];
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Peq_T = Peq['T'];
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Peq_G = Peq['G'];
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memset(Peq, 0, sizeof(Word)* 256);
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Peq['A'] = Peq_A;
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Peq['C'] = Peq_C;
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Peq['T'] = Peq_T;
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Peq['G'] = Peq_G;
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Word Mask = ((Word)1 << (errthold << 1));
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Word VP = 0;
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Word VN = 0;
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Word X = 0;
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Word D0 = 0;
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Word HN = 0;
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Word HP = 0;
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i = 0;
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int err = 0;
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Word err_mask = (Word)1;
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///band_down = 2k
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///i_bd = 2k
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///int i_bd = i + band_down;
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int i_bd = (errthold << 1);
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int last_high = (errthold << 1);
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/// t_length_1 = SEQ_LENGTH - 1
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int t_length_1 = t_length - 1;
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//while(i<t_length)
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while (i<t_length_1)
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{
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///pattern[0]ÔÚPeq[2k], ¶øpattern[2k]ÔÚPeq[0]
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X = Peq[text[i]] | VN;
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D0 = ((VP + (X&VP)) ^ VP) | X;
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HN = VP&D0;
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HP = VN | ~(VP | D0);
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X = D0 >> 1;
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VN = X&HP;
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VP = HN | ~(X | HP);
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///Èç¹ûб¶Ô½ÇÏß·½ÏòÆ¥ÅäÔòD0ÊÇ1
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///Èç¹û²»Æ¥ÅäÔòD0ÊÇ0
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///Õâ¸öÒâ˼ÊÇÈç¹û×îÉÏÃæÄÇÌõ¶Ô½ÇÏßÉϵÄб¶Ô½ÇÏß·½Ïò·¢ÉúÎóÅä,ÔòÖ´ÐÐÄÚ²¿³ÌÐò
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///
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if (!(D0&err_mask))
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{
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++err;
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///¼´Ê¹È«²¿µÝ¼õ£¬Ò²¾Í¼õ2k
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if ((err - last_high)>errthold)
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return -1;
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}
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///pattern[0]ÔÚPeq[2k], ¶øpattern[2k]ÔÚPeq[0]
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//ÓÒÒÆʵ¼ÊÉÏÊÇ°Ñpattern[0]ÒƵôÁË
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Peq['A'] = Peq['A'] >> 1;
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Peq['C'] = Peq['C'] >> 1;
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Peq['G'] = Peq['G'] >> 1;
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Peq['T'] = Peq['T'] >> 1;
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||
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||
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++i;
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++i_bd;
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///ÕâÊÇ°ÑеÄpattern[2k]¼Ó½øÀ´, ÕâòËÆÊǼӵ½Peq[2k]ÉÏÁË
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Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
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||
|
||
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Peq['T'] = Peq['T'] | Peq['C'];
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||
}
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||
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||
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||
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///fprintf(stderr, "sucess(1)\n");
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||
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||
///Õâ¸öÑ»·ÄóöÀ´ÊÇΪÁË·ÀÖ¹ÄÚ´æй¶
|
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///ÆäʵҲ¾ÍÊÇÑ»·ÀïµÄ×îºóÒ»ÐÐÓï¾ä°É
|
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///ÍêÈ«¿ÉÒÔ°ÑpatternÔö´óһλ
|
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///²»¹ýÕâÑùÒ²ºÃ£¬¿ÉÒÔ¼õÉÙ¼ÆË㿪Ïú
|
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X = Peq[text[i]] | VN;
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||
D0 = ((VP + (X&VP)) ^ VP) | X;
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||
HN = VP&D0;
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HP = VN | ~(VP | D0);
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||
X = D0 >> 1;
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||
VN = X&HP;
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||
VP = HN | ~(X | HP);
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||
if (!(D0&err_mask))
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||
{
|
||
++err;
|
||
if ((err - last_high)>errthold)
|
||
return -1;
|
||
}
|
||
|
||
|
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|
||
|
||
|
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////fprintf(stderr, "sucess(2)\n");
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/// last_high = 2k
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/// site = (SEQ_LENGTH + 2k) - 2k -1
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/// site = SEQ_LENGTH - 1
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||
///´ËʱÕâ¸ösiteòËÆÊÇ×îÉÏÃæÄÇÌõ¶Ô½ÇÏßµÄλÖÃ
|
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///int site = p_length - last_high - 1;
|
||
int site = t_length - 1;
|
||
int return_site = -1;
|
||
if ((err <= errthold) && (err<=*return_err))
|
||
{
|
||
*return_err = err;
|
||
return_site = site;
|
||
}
|
||
int i_last = i;
|
||
i = 0;
|
||
|
||
|
||
|
||
|
||
while (i<errthold)
|
||
{
|
||
err = err + ((VP >> i)&(Word)1);
|
||
err = err - ((VN >> i)&(Word)1);
|
||
++i;
|
||
|
||
if ((err <= errthold) && (err <= *return_err))
|
||
{
|
||
*return_err = err;
|
||
return_site = site + i;
|
||
}
|
||
}
|
||
|
||
|
||
unsigned int ungap_err;
|
||
ungap_err = err;
|
||
|
||
|
||
while (i<last_high)
|
||
{
|
||
err = err + ((VP >> i)&(Word)1);
|
||
err = err - ((VN >> i)&(Word)1);
|
||
++i;
|
||
|
||
if ((err <= errthold) && (err<=*return_err))
|
||
{
|
||
*return_err = err;
|
||
return_site = site + i;
|
||
}
|
||
|
||
|
||
|
||
|
||
}
|
||
|
||
|
||
if ((ungap_err <= errthold) && (ungap_err == *return_err))
|
||
{
|
||
return_site = site + errthold;
|
||
}
|
||
|
||
return return_site;
|
||
|
||
}
|
||
|
||
int Reserve_Banded_BPM_new(char *pattern,int p_length,char *text,int t_length,
|
||
unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length,int* return_err, int thread_id)
|
||
{
|
||
|
||
Word Peq[128];
|
||
char Peq_index[4]= {'A','C','G','T'};
|
||
int symbol = 0;
|
||
int r;
|
||
Word tmp_Peq_1=(Word)1;
|
||
|
||
|
||
Peq['A']=(Word)0;
|
||
Peq['T']=(Word)0;
|
||
Peq['G']=(Word)0;
|
||
Peq['C']=(Word)0;
|
||
Word Peq_A;
|
||
Word Peq_T;
|
||
Word Peq_C;
|
||
Word Peq_G;
|
||
|
||
for (r =0; r<band_length; r++)
|
||
{
|
||
Peq[pattern[r]]=Peq[pattern[r]]|tmp_Peq_1;
|
||
tmp_Peq_1=tmp_Peq_1<<1;
|
||
}
|
||
Peq_A=Peq['A'];
|
||
Peq_C=Peq['C'];
|
||
Peq_T=Peq['T'];
|
||
Peq_G=Peq['G'];
|
||
|
||
for(symbol = 0; symbol < 128; symbol++)
|
||
{
|
||
Peq[symbol]=(Word)0;
|
||
//jump_c[symbol]=128;
|
||
}
|
||
Peq['A']=Peq_A;
|
||
Peq['C']=Peq_C;
|
||
Peq['T']=Peq_T;
|
||
Peq['G']=Peq_G;
|
||
|
||
|
||
Word Mask_Pre=(Word)1<<(band_length-2);
|
||
Word Mask=(Word)1<<(band_length-1);
|
||
Word VP=0;
|
||
Word VN=0;
|
||
Word X=0;
|
||
Word D0=0;
|
||
Word HN=0;
|
||
Word HP=0;
|
||
|
||
|
||
int s=0;
|
||
int i = 0;
|
||
int j=0;
|
||
|
||
int bound=band_length-2-band_down;
|
||
int err=0;
|
||
|
||
Word err_mask=(Word)1;
|
||
int s1=band_length-2;
|
||
int i_bd=i+band_down;
|
||
int last_high=band_length-t_length+p_length-band_down-1;
|
||
int t_length_1=t_length-1;
|
||
//while(i<t_length)
|
||
while(i<t_length_1)
|
||
{
|
||
|
||
X=Peq[text[i]]|VN;
|
||
|
||
D0=((VP+(X&VP))^VP)|X;
|
||
|
||
HN=VP&D0;
|
||
HP=VN|~(VP|D0);
|
||
|
||
X=D0>>1;
|
||
VN=X&HP;
|
||
VP=HN|~(X|HP);
|
||
if(!(D0&err_mask))
|
||
{
|
||
++err;
|
||
if((err-last_high)>errthold)
|
||
return -1;
|
||
}
|
||
|
||
Peq['A']=Peq['A']>>1;
|
||
Peq['C']=Peq['C']>>1;
|
||
Peq['G']=Peq['G']>>1;
|
||
Peq['T']=Peq['T']>>1;
|
||
|
||
|
||
++i;
|
||
++i_bd;
|
||
Peq[pattern[i_bd]]=Peq[pattern[i_bd]]|Mask;
|
||
}
|
||
|
||
|
||
///这个循环拿出来是为了防止内存泄露
|
||
|
||
X=Peq[text[i]]|VN;
|
||
D0=((VP+(X&VP))^VP)|X;
|
||
HN=VP&D0;
|
||
HP=VN|~(VP|D0);
|
||
X=D0>>1;
|
||
VN=X&HP;
|
||
VP=HN|~(X|HP);
|
||
if(!(D0&err_mask))
|
||
{
|
||
++err;
|
||
if((err-last_high)>errthold)
|
||
return -1;
|
||
}
|
||
|
||
|
||
int site=p_length-last_high-1;
|
||
int return_site=-1;
|
||
if((err<=errthold)&&(err<*return_err))
|
||
{
|
||
*return_err=err;
|
||
return_site=site;
|
||
}
|
||
int i_last=i;
|
||
i=0;
|
||
while(i<last_high)
|
||
{
|
||
err=err+((VP>>i)&(Word)1);
|
||
err=err-((VN>>i)&(Word)1);
|
||
++i;
|
||
|
||
if((err<=errthold)&&(err<*return_err))
|
||
{
|
||
*return_err=err;
|
||
return_site=site+i;
|
||
}
|
||
|
||
|
||
}
|
||
return return_site;
|
||
|
||
}
|