mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-10 14:40:57 +08:00
extend ed alignment
This commit is contained in:
chhylp123
+911
-2
@@ -8,9 +8,12 @@
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#include <string.h>
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#include <stdlib.h>
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#include <stdio.h>
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#include "kvec.h"
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extern const unsigned char seq_nt4_table[256];
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typedef uint64_t Word;
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typedef uint32_t Word_32;
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typedef struct {size_t n, m; uint16_t *a; } asg16_v;
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inline void get_error(int t_length, int errthold, int init_err, Word VP, Word VN,
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unsigned int* return_err, int* back_site)
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@@ -208,6 +211,151 @@ unsigned int* return_err, int* return_p_end, int* return_t_end)
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return (*return_t_end);
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}
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inline int Reserve_Banded_BPM_Extension_REV
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(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
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unsigned int* return_err, int* return_p_end, int* return_t_end)
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{
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(*return_err) = (unsigned int)-1;
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(*return_p_end) = -1;
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(*return_t_end) = -1;
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Word Peq[256];
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unsigned int line_error = (unsigned int)-1;
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int return_site;
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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[(uint8_t)'A'] = (Word)0;
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Peq[(uint8_t)'T'] = (Word)0;
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Peq[(uint8_t)'G'] = (Word)0;
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Peq[(uint8_t)'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[(uint8_t)pattern[p_length-i-1]] = Peq[(uint8_t)pattern[p_length-i-1]] | tmp_Peq_1;
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tmp_Peq_1 = tmp_Peq_1 << 1;
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}
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Peq_A = Peq[(uint8_t)'A'];
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Peq_C = Peq[(uint8_t)'C'];
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Peq_T = Peq[(uint8_t)'T'];
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Peq_G = Peq[(uint8_t)'G'];
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memset(Peq, 0, sizeof(Word)* 256);
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Peq[(uint8_t)'A'] = Peq_A;
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Peq[(uint8_t)'C'] = Peq_C;
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Peq[(uint8_t)'T'] = Peq_T;
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Peq[(uint8_t)'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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int i_bd = (errthold << 1);
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int last_high = (errthold << 1);
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int t_length_1 = t_length - 1;
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while (i<t_length_1)
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{
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X = Peq[(uint8_t)text[t_length-i-1]] | 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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{
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return (*return_t_end);
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}
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}
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get_error(i + 1, errthold, err, VP, VN, &line_error, &return_site);
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if(line_error != (unsigned int)-1)
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{
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(*return_t_end) = t_length-i-1;
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(*return_p_end) = p_length-return_site-1;
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(*return_err) = line_error;
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}
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Peq[(uint8_t)'A'] = Peq[(uint8_t)'A'] >> 1;
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Peq[(uint8_t)'C'] = Peq[(uint8_t)'C'] >> 1;
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Peq[(uint8_t)'G'] = Peq[(uint8_t)'G'] >> 1;
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Peq[(uint8_t)'T'] = Peq[(uint8_t)'T'] >> 1;
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++i;
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++i_bd;
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Peq[(uint8_t)pattern[p_length-i_bd-1]] = Peq[(uint8_t)pattern[p_length-i_bd-1]] | Mask;
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}
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X = Peq[(uint8_t)text[t_length-i-1]] | 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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{
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return (*return_t_end);
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}
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}
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///i = t_length - 1
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get_error(i + 1, errthold, err, VP, VN, &line_error, &return_site);
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if(line_error != (unsigned int)-1)
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{
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(*return_t_end) = t_length-i-1;
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(*return_p_end) = p_length-return_site-1;
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(*return_err) = line_error;
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}
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return (*return_t_end);
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}
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inline void reverse_string(char* str, int strLen)
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{
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int i, Len;
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@@ -267,7 +415,494 @@ int* return_t_end, int* return_aligned_t_len)
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}
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}
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///p_length might be samller than t_length + 2 * errthold
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/// pattern is longer than text
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inline int32_t ed_band_cal_semi(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *re_err)
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{
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(*re_err) = INT32_MAX;
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Word Peq[5] = {0}, mm = (Word)1, VP = 0, VN = 0, X = 0, D0 = 0, HN = 0, HP = 0;
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int32_t bd = (thre<<1)+1, i, err = 0, i_bd = (thre<<1), last_high = (thre<<1), tn0 = tn - 1;
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int32_t cut = thre+last_high;
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for (i = 0; i < bd; i++) {
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Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
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}
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///should make Peq[4] = 0 if N is always an error
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Peq[4] = 0;
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i = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char
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while (i < tn0) {
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X = Peq[seq_nt4_table[(uint8_t)tstr[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&(1ULL))) {
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++err;
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if (err>cut) return -1;
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}
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Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1; ///Peq[4] >>= 1;
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++i; ++i_bd;
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Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;
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}
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X = Peq[seq_nt4_table[(uint8_t)tstr[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&(1ULL))) {
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++err;
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if (err>cut) return -1;
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}
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int32_t site = tn - 1, end = -1;///up bound
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///in most cases, ai = (thre<<1)
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int32_t ai = pn - tn, uge = INT32_MAX;
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if ((err <= thre) && (err<=(*re_err))) {
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*re_err = err; end = site;
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}
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i = 0;
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while (i < ai) {
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err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL)); ++i;
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if ((err <= thre) && (err <= (*re_err))) {
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*re_err = err; end = site + i;
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}
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if(i == thre) uge = err;
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}
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if((uge<=thre) && (uge == (*re_err))) end = site + thre;
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return end;
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}
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inline void print_bit(Word z, int64_t w, const char *cmd)
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{
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int64_t k;//, w = (sizeof(Word)<<3);
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fprintf(stderr, "%s\t", cmd);
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for (k = 0; k < w; k++) fprintf(stderr, "%llu", (z>>k)&(1ULL));
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fprintf(stderr, "\n");
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}
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inline void print_bits(Word *az, int64_t w, const char *cmd)
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{
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int64_t k, m, s = (sizeof(*az)<<3), sw = (w/s) + (!!(w%s)), ks;
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fprintf(stderr, "%s\t", cmd);
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for (m = k = 0; m < sw && k < w; m++) {
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for (ks = 0; ks < s && k < w; ks++, k++) fprintf(stderr, "%llu", (az[m]>>ks)&(1ULL));
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}
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fprintf(stderr, "\n");
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}
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inline int32_t ed_band_cal_global(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre)
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{
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if((pn > tn + thre) || (tn > pn + thre)) return INT32_MAX;
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if((pn < thre + 1) || (tn < thre + 1)) return INT32_MAX;
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Word Peq[5] = {0}, mm, VP = 0, VN = 0, X = 0, D0 = 0, HN = 0, HP = 0;
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int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd = thre+1, i_bd = thre;
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// fprintf(stderr, "\n[M::%s::]\n", __func__);
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for (i = 0, mm = (((Word)1)<<thre); i < bd; i++) {
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Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
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}
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Peq[4] = 0;
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err = thre;
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VN = (((Word)1)<<(thre))-1;
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VP = (((Word)1)<<((thre<<1)+1))-1; VP ^= VN;
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// print_bit(Peq[0], (thre<<1)+1, "Peq[A]");
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// print_bit(Peq[1], (thre<<1)+1, "Peq[C]");
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// print_bit(Peq[2], (thre<<1)+1, "Peq[G]");
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// print_bit(Peq[3], (thre<<1)+1, "Peq[T]");
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// print_bit(Peq[4], (thre<<1)+1);
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// print_bit(VN, (thre<<1)+1, "VN");
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// print_bit(VP, (thre<<1)+1, "VP");
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///should make Peq[4] = 0 if N is always an error
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i = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char
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while (i < tn0) {
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X = Peq[seq_nt4_table[(uint8_t)tstr[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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// fprintf(stderr, "\n[M::%s::i->%d]\n", __func__, i);
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// print_bit(VN, (thre<<1)+1, "VN");
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// print_bit(VP, (thre<<1)+1, "VP");
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// print_bit(HN, (thre<<1)+1, "HN");
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// print_bit(HP, (thre<<1)+1, "HP");
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// print_bit(D0, (thre<<1)+1, "D0");
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if (!(D0&(1ULL))) {
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++err;
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if (err>cut) return INT32_MAX;
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}
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// fprintf(stderr, "[M::%s::i->%d] err->%d\n", __func__, i, err);
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Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1; ///Peq[4] >>= 1;
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++i; ++i_bd;
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if(i_bd < pn) {
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Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;
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}
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// if(i < pn) Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm;
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}
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X = Peq[seq_nt4_table[(uint8_t)tstr[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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// fprintf(stderr, "\n[M::%s::i->%d]\n", __func__, i);
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// print_bit(VN, (thre<<1)+1, "VN");
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// print_bit(VP, (thre<<1)+1, "VP");
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// print_bit(HN, (thre<<1)+1, "HN");
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// print_bit(HP, (thre<<1)+1, "HP");
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// print_bit(D0, (thre<<1)+1, "D0");
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if (!(D0&(1ULL))) {
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++err;
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if (err>cut) return INT32_MAX;
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}
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// fprintf(stderr, "[M::%s::i->%d] err->%d\n", __func__, i, err);
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int32_t site = tn - 1 - thre;///up bound
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for (cut = pn - 1, i = 0; site < cut; site++, i++) {
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// fprintf(stderr, "+[M::%s::site->%d] err->%d\n", __func__, site, err);
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err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL));
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// fprintf(stderr, "-[M::%s::site->%d] err->%d\n", __func__, site, err);
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}
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if (site == cut && err <= thre) return err;
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return INT32_MAX;
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}
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typedef uint64_t w_sig;
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typedef struct {w_sig a[2];} w128_t;
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#define bitw (6)
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#define bitwbit (64)
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#define bitz (63)
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// typedef uint32_t w_sig;
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// typedef struct {w_sig a[2];} w128_t;
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// #define bitw (5)
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// #define bitwbit (32)
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// #define bitz (31)
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#define w128_bit(x, b) ((x).a[((b)>>bitw)]|=(((w_sig)1)<<((b)&bitz)))
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#define w128_clear(x) ((x).a[0]=(x).a[1]=0)
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#define w128_self_not(x) ((x).a[0]=~(x).a[0], \
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(x).a[1]=~(x).a[1])
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#define w128_self_or(x, y) ((x).a[0]|=(y).a[0], \
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(x).a[1]|=(y).a[1])
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#define w128_or(r, x, y) ((r).a[0] = (x).a[0]|(y).a[0], \
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(r).a[1] = (x).a[1]|(y).a[1])
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#define w128_and(r, x, y) ((r).a[0] = (x).a[0]&(y).a[0], \
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(r).a[1] = (x).a[1]&(y).a[1])
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#define w128_self_xor(x, y) ((x).a[0]^=(y).a[0], \
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(x).a[1]^=(y).a[1])
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// #define w128_self_lsft_l(x, l) ((x).a[1] = ((x).a[1]<<(l))|((x).a[0]>>(bitwbit-(l))), \
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// (x).a[0] <<= (l))
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#define w128_self_lsft_1(x) ((x).a[1] = ((x).a[1]<<1)|((x).a[0]>>bitz), \
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(x).a[0] <<= 1)
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#define w128_self_rsft_1(x) ((x).a[0] = ((x).a[0]>>1)|((x).a[1]<<bitz), \
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(x).a[1] >>= 1)
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#define w128_self_add(x, y) ((x).a[0]+=(y).a[0], \
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(x).a[1]+=(y).a[1]+((x).a[0]<(y).a[0]))
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#define w128_set_bit_lsub(x, l) do { \
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(x).a[0] = (w_sig)-1, (x).a[1] = 0; \
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if((l) <= bitwbit) (x).a[0] = (((w_sig)1)<<(l))-1; \
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else (x).a[1] = (((w_sig)1)<<((l)-bitwbit))-1;\
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} while (0) \
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#define ed_core_w128(RE) { \
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/**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\
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c = seq_nt4_table[(uint8_t)tstr[i]]; w128_or(X, Peq[c], VN);\
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/**D0 = ((VP + (X&VP)) ^ VP) | X;**/\
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w128_and(D0, X, VP);\
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w128_self_add(D0, VP);\
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w128_self_xor(D0, VP);\
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w128_self_or(D0, X);\
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/**HN = VP&D0;**/\
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w128_and(HN, VP, D0);\
|
||||
/**HP = VN | ~(VP | D0);**/\
|
||||
w128_or(HP, VP, D0);\
|
||||
w128_self_not(HP);\
|
||||
w128_self_or(HP, VN);\
|
||||
/**X = D0 >> 1;**/\
|
||||
X = D0; w128_self_rsft_1(X);\
|
||||
/**VN = X&HP;**/\
|
||||
w128_and(VN, X, HP);\
|
||||
/**VP = HN | ~(X | HP);**/\
|
||||
w128_or(VP, X, HP);\
|
||||
w128_self_not(VP);\
|
||||
w128_self_or(VP, HN);\
|
||||
/**if (!(D0&(1ULL)))**/\
|
||||
if (!(D0.a[0]&(1ULL))) {\
|
||||
++err;\
|
||||
if (err>cut) return RE;\
|
||||
}\
|
||||
/** Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;**/\
|
||||
w128_self_rsft_1(Peq[0]); w128_self_rsft_1(Peq[1]);\
|
||||
w128_self_rsft_1(Peq[2]); w128_self_rsft_1(Peq[3]);\
|
||||
}
|
||||
|
||||
inline int32_t ed_band_cal_global_128bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre)
|
||||
{
|
||||
if((pn > tn + thre) || (tn > pn + thre)) return INT32_MAX;
|
||||
if((pn < thre + 1) || (tn < thre + 1)) return INT32_MAX;
|
||||
w128_t Peq[5], mm, VP, VN, X, D0, HN, HP; uint8_t c;
|
||||
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd = thre+1, i_bd = thre;
|
||||
w128_clear(Peq[0]); w128_clear(Peq[1]); w128_clear(Peq[2]); w128_clear(Peq[3]); w128_clear(Peq[4]);
|
||||
|
||||
w128_clear(mm); w128_bit(mm, thre); ///mm = (((Word)1)<<thre)
|
||||
for (i = 0; i < bd; i++) {
|
||||
w128_self_or(Peq[seq_nt4_table[(uint8_t)pstr[i]]], mm); w128_self_lsft_1(mm);
|
||||
// Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
|
||||
}
|
||||
w128_clear(Peq[4]);
|
||||
err = thre;
|
||||
w128_set_bit_lsub(VN, thre); ///VN = (((Word)1)<<(thre))-1;
|
||||
w128_set_bit_lsub(VP, (thre<<1)+1); ///VP = (((Word)1)<<((thre<<1)+1))-1;
|
||||
w128_self_xor(VP, VN); ///VP ^= VN;
|
||||
|
||||
// print_bits(Peq[0].a, (thre<<1)+1, "-Peq[A]");
|
||||
// print_bits(Peq[1].a, (thre<<1)+1, "-Peq[C]");
|
||||
// print_bits(Peq[2].a, (thre<<1)+1, "-Peq[G]");
|
||||
// print_bits(Peq[3].a, (thre<<1)+1, "-Peq[T]");
|
||||
// print_bits(VN.a, (thre<<1)+1, "-VN");
|
||||
// print_bits(VP.a, (thre<<1)+1, "-VP");
|
||||
|
||||
///should make Peq[4] = 0 if N is always an error
|
||||
i = 0;
|
||||
///for the incoming char/last char
|
||||
w128_clear(mm); w128_bit(mm, (thre<<1)); ///mm = ((Word)1 << (thre<<1));
|
||||
//VP + ((Peq|VN)&VP)
|
||||
while (i < tn0) {
|
||||
///X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
|
||||
c = seq_nt4_table[(uint8_t)tstr[i]]; w128_or(X, Peq[c], VN);
|
||||
|
||||
///D0 = ((VP + (X&VP)) ^ VP) | X;
|
||||
w128_and(D0, X, VP);
|
||||
w128_self_add(D0, VP);
|
||||
w128_self_xor(D0, VP);
|
||||
w128_self_or(D0, X);
|
||||
|
||||
// HN = VP&D0;
|
||||
w128_and(HN, VP, D0);
|
||||
// HP = VN | ~(VP | D0);
|
||||
w128_or(HP, VP, D0);
|
||||
w128_self_not(HP);
|
||||
w128_self_or(HP, VN);
|
||||
|
||||
// X = D0 >> 1;
|
||||
X = D0; w128_self_rsft_1(X);
|
||||
// VN = X&HP;
|
||||
w128_and(VN, X, HP);
|
||||
// VP = HN | ~(X | HP);
|
||||
w128_or(VP, X, HP);
|
||||
w128_self_not(VP);
|
||||
w128_self_or(VP, HN);
|
||||
|
||||
|
||||
//if (!(D0&(1ULL)))
|
||||
if (!(D0.a[0]&(1ULL))) {
|
||||
++err;
|
||||
if (err>cut) return INT32_MAX;
|
||||
}
|
||||
// fprintf(stderr, "[M::%s::i->%d] err->%d\n", __func__, i, err);
|
||||
|
||||
// Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
|
||||
w128_self_rsft_1(Peq[0]); w128_self_rsft_1(Peq[1]);
|
||||
w128_self_rsft_1(Peq[2]); w128_self_rsft_1(Peq[3]);
|
||||
|
||||
++i; ++i_bd;
|
||||
if(i_bd < pn) {
|
||||
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
|
||||
///if(c < 4) Peq[c] |= mm;
|
||||
if(c < 4) w128_self_or(Peq[c], mm);
|
||||
}
|
||||
}
|
||||
|
||||
// X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
|
||||
c = seq_nt4_table[(uint8_t)tstr[i]]; w128_or(X, Peq[c], VN);
|
||||
// D0 = ((VP + (X&VP)) ^ VP) | X;
|
||||
w128_and(D0, X, VP);
|
||||
w128_self_add(D0, VP);
|
||||
w128_self_xor(D0, VP);
|
||||
w128_self_or(D0, X);
|
||||
// HN = VP&D0;
|
||||
w128_and(HN, VP, D0);
|
||||
// HP = VN | ~(VP | D0);
|
||||
w128_or(HP, VP, D0);
|
||||
w128_self_not(HP);
|
||||
w128_self_or(HP, VN);
|
||||
// X = D0 >> 1;
|
||||
X = D0; w128_self_rsft_1(X);
|
||||
// VN = X&HP;
|
||||
w128_and(VN, X, HP);
|
||||
// VP = HN | ~(X | HP);
|
||||
w128_or(VP, X, HP);
|
||||
w128_self_not(VP);
|
||||
w128_self_or(VP, HN);
|
||||
|
||||
// if (!(D0&(1ULL))) {
|
||||
if (!(D0.a[0]&(1ULL))) {
|
||||
++err;
|
||||
if (err>cut) return INT32_MAX;
|
||||
}
|
||||
// fprintf(stderr, "[M::%s::i->%d] err->%d\n", __func__, i, err);
|
||||
|
||||
int32_t site = tn - 1 - thre;///up bound
|
||||
for (cut = pn - 1, i = 0; site < cut; site++, i++) {
|
||||
// err += ((VP >> i)&(1ULL));
|
||||
err += VP.a[0]&(1ULL); w128_self_rsft_1(VP);
|
||||
// err -= ((VN >> i)&(1ULL));
|
||||
err -= VN.a[0]&(1ULL); w128_self_rsft_1(VN);
|
||||
}
|
||||
|
||||
if (site == cut && err <= thre) return err;
|
||||
return INT32_MAX;
|
||||
}
|
||||
|
||||
inline int32_t ed_band_cal_semi_128bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *re_err)
|
||||
{
|
||||
(*re_err) = INT32_MAX;
|
||||
w128_t Peq[5], mm, VP, VN, X, D0, HN, HP;
|
||||
//Peq[5] = {0}, mm = (Word)1, VP = 0, VN = 0, X, D0, HN, HP;
|
||||
w128_clear(VP); w128_clear(VN); w128_clear(mm); w128_bit(mm, 0);
|
||||
w128_clear(Peq[0]); w128_clear(Peq[1]); w128_clear(Peq[2]); w128_clear(Peq[3]); w128_clear(Peq[4]);
|
||||
int32_t bd = (thre<<1)+1, i, err = 0, i_bd = (thre<<1), last_high = (thre<<1), tn0 = tn - 1;
|
||||
int32_t cut = thre+last_high; uint8_t c;
|
||||
|
||||
for (i = 0; i < bd; i++) {
|
||||
w128_self_or(Peq[seq_nt4_table[(uint8_t)pstr[i]]], mm); w128_self_lsft_1(mm);
|
||||
// Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
|
||||
}
|
||||
///should make Peq[4] = 0 if N is always an error
|
||||
// Peq[4] = 0;
|
||||
w128_clear(Peq[4]);
|
||||
//mm = ((Word)1 << (thre<<1));///for the incoming char/last char
|
||||
w128_clear(mm); w128_bit(mm, (thre<<1));
|
||||
|
||||
i = 0;
|
||||
while (i < tn0) {
|
||||
// X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
|
||||
c = seq_nt4_table[(uint8_t)tstr[i]]; w128_or(X, Peq[c], VN);
|
||||
|
||||
// D0 = ((VP + (X&VP)) ^ VP) | X;
|
||||
w128_and(D0, X, VP);
|
||||
w128_self_add(D0, VP);
|
||||
w128_self_xor(D0, VP);
|
||||
w128_self_or(D0, X);
|
||||
|
||||
// HN = VP&D0;
|
||||
w128_and(HN, VP, D0);
|
||||
// HP = VN | ~(VP | D0);
|
||||
w128_or(HP, VP, D0);
|
||||
w128_self_not(HP);
|
||||
w128_self_or(HP, VN);
|
||||
|
||||
// X = D0 >> 1;
|
||||
X = D0; w128_self_rsft_1(X);
|
||||
// VN = X&HP;
|
||||
w128_and(VN, X, HP);
|
||||
// VP = HN | ~(X | HP);
|
||||
w128_or(VP, X, HP);
|
||||
w128_self_not(VP);
|
||||
w128_self_or(VP, HN);
|
||||
|
||||
// if (!(D0&(1ULL))) {
|
||||
if (!(D0.a[0]&(1ULL))) {
|
||||
++err;
|
||||
if (err>cut) return -1;
|
||||
}
|
||||
|
||||
// Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
|
||||
w128_self_rsft_1(Peq[0]); w128_self_rsft_1(Peq[1]);
|
||||
w128_self_rsft_1(Peq[2]); w128_self_rsft_1(Peq[3]);
|
||||
|
||||
++i; ++i_bd;
|
||||
// Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;
|
||||
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
|
||||
if(c < 4) w128_self_or(Peq[c], mm);
|
||||
}
|
||||
|
||||
// X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
|
||||
c = seq_nt4_table[(uint8_t)tstr[i]]; w128_or(X, Peq[c], VN);
|
||||
// D0 = ((VP + (X&VP)) ^ VP) | X;
|
||||
w128_and(D0, X, VP);
|
||||
w128_self_add(D0, VP);
|
||||
w128_self_xor(D0, VP);
|
||||
w128_self_or(D0, X);
|
||||
// HN = VP&D0;
|
||||
w128_and(HN, VP, D0);
|
||||
// HP = VN | ~(VP | D0);
|
||||
w128_or(HP, VP, D0);
|
||||
w128_self_not(HP);
|
||||
w128_self_or(HP, VN);
|
||||
// X = D0 >> 1;
|
||||
X = D0; w128_self_rsft_1(X);
|
||||
// VN = X&HP;
|
||||
w128_and(VN, X, HP);
|
||||
// VP = HN | ~(X | HP);
|
||||
w128_or(VP, X, HP);
|
||||
w128_self_not(VP);
|
||||
w128_self_or(VP, HN);
|
||||
// if (!(D0&(1ULL))) {
|
||||
if (!(D0.a[0]&(1ULL))) {
|
||||
++err;
|
||||
if (err>cut) return -1;
|
||||
}
|
||||
|
||||
int32_t site = tn - 1, end = -1;///up bound
|
||||
///in most cases, ai = (thre<<1)
|
||||
int32_t ai = pn - tn, uge = INT32_MAX;
|
||||
if ((err <= thre) && (err<=(*re_err))) {
|
||||
*re_err = err; end = site;
|
||||
}
|
||||
i = 0;
|
||||
|
||||
while (i < ai) {
|
||||
// err += ((VP >> i)&(1ULL));
|
||||
err += VP.a[0]&(1ULL); w128_self_rsft_1(VP);
|
||||
// err -= ((VN >> i)&(1ULL));
|
||||
err -= VN.a[0]&(1ULL); w128_self_rsft_1(VN);
|
||||
++i;
|
||||
if ((err <= thre) && (err <= (*re_err))) {
|
||||
*re_err = err; end = site + i;
|
||||
}
|
||||
if(i == thre) uge = err;
|
||||
}
|
||||
|
||||
if((uge<=thre) && (uge == (*re_err))) end = site + thre;
|
||||
return end;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
@@ -277,7 +912,9 @@ inline int Reserve_Banded_BPM
|
||||
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold, unsigned int* return_err)
|
||||
{
|
||||
(*return_err) = (unsigned int)-1;
|
||||
|
||||
// int32_t rerr, rsite = ed_band_cal_semi_128bit(pattern, p_length, text, t_length, errthold, &rerr);
|
||||
// if(rsite >= 0) (*return_err) = rerr;
|
||||
// return rsite;
|
||||
Word Peq[256];
|
||||
|
||||
int band_length = (errthold << 1) + 1;
|
||||
@@ -888,7 +1525,6 @@ inline int Reserve_Banded_BPM_PATH
|
||||
return return_site;
|
||||
}
|
||||
|
||||
|
||||
////four patterns have the same p_length
|
||||
inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *pattern3, char *pattern4, int p_length, char *text, int t_length,
|
||||
int* return_sites, unsigned int* return_sites_error, unsigned short errthold, __m128i* Peq_SSE)
|
||||
@@ -1198,4 +1834,277 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
|
||||
}
|
||||
|
||||
|
||||
#define EAC_M 0
|
||||
#define MIS_M 1
|
||||
#define MOR_YP 2
|
||||
#define MOR_XT 3
|
||||
|
||||
inline void push_trace(asg16_v *res, uint16_t c, uint32_t len)
|
||||
{
|
||||
uint16_t p; c <<= 14;
|
||||
while (len >= (0x3fff)) {
|
||||
p = (c + (0x3fff)); kv_push(uint16_t, *res, p); len -= (0x3fff);
|
||||
}
|
||||
if(len) {
|
||||
p = (c + len); kv_push(uint16_t, *res, p);
|
||||
}
|
||||
}
|
||||
|
||||
// void move_trace_gap(uint16_t *trace, int32_t trace_n, int32_t trace_i,
|
||||
// char *pstr, int32_t pi, char *tstr, int32_t ti, int32_t *err)
|
||||
// {
|
||||
// uint16_t c = trace[trace_i]>>14, l = (trace[trace_i]<<2)>>2;
|
||||
// if(c != 3 && c != 2) return;
|
||||
// trace_i--;
|
||||
// if(c == 3) pi--;
|
||||
// else if(c == 2) ti--;
|
||||
|
||||
|
||||
// if()
|
||||
|
||||
// }
|
||||
|
||||
// void adjust_trace(uint16_t *trace, int32_t *trace_n, int32_t *p_beg, int32_t *p_end, int32_t *err, char *pstr, char *tstr)
|
||||
// {
|
||||
// if((*err) == 0) return;
|
||||
// int32_t i, pi, ti; uint16_t c, l;
|
||||
// for (i = 0; i < (*trace_n) && (trace[i]>>14) == 1; i++) {
|
||||
// trace[i] <<= 2; trace[i] >>= 2; trace[i] += (((uint16_t)3)<<14);
|
||||
// l = (trace[i]<<2)>>2; (*p_beg) += l;
|
||||
// }
|
||||
// for (i = (*trace_n) - 1; i >= 0 && (trace[i]>>14) == 1; i--) {
|
||||
// trace[i] <<= 2; trace[i] >>= 2; trace[i] += (((uint16_t)3)<<14);
|
||||
// l = (trace[i]<<2)>>2; (*p_end) -= l;
|
||||
// }
|
||||
|
||||
// i = 0; pi = (*p_beg); ti = 0;
|
||||
// for (i = 0; i < (*trace_n); i++) {
|
||||
// c = trace[i]>>14; l = (trace[i]<<2)>>2;
|
||||
// if(c == 0 || c == 1) {
|
||||
// pi += l; ti += l;
|
||||
// } else if(c == 2) {
|
||||
// // move_trace_gap(trace, *trace_n, i, pstr, pi, tstr, ti, err);
|
||||
// pi += l;
|
||||
// } else if(c == 3) {
|
||||
// // move_trace_gap(trace, *trace_n, i, pstr, pi, tstr, ti, err);
|
||||
// ti += l;
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
|
||||
inline int32_t ungap_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t know_err, int32_t know_end,
|
||||
int32_t *r_err, int32_t *r_beg, asg16_v *cigar, int32_t *cigar_l)
|
||||
{
|
||||
int32_t cn = cigar->n, pk, tk, e, l;
|
||||
(*r_err) = (*r_beg) = INT32_MAX; (*cigar_l) = 0;
|
||||
if(know_err < 0 || know_end < 0) return -1;
|
||||
if(know_err == 0) {
|
||||
push_trace(cigar, EAC_M, tn);
|
||||
(*r_err) = know_err; (*r_beg) = know_end + 1 - tn; (*cigar_l) = cigar->n - cn;
|
||||
return know_end;
|
||||
}
|
||||
|
||||
pk = know_end+1-tn; tk = 0; e = 0;
|
||||
for (l = 0; tk < tn; tk++, pk++) {
|
||||
if(pstr[pk]!=tstr[tk]) {
|
||||
e++; if(e > know_err) break;
|
||||
if(tk > l) push_trace(cigar, EAC_M, tk-l);
|
||||
push_trace(cigar, MIS_M, 1); l = tk + 1;
|
||||
}
|
||||
}
|
||||
if(tk == tn) {
|
||||
if(tk > l) push_trace(cigar, EAC_M, tk-l);
|
||||
(*r_err) = know_err; (*r_beg) = know_end + 1 - tn; (*cigar_l) = cigar->n - cn;
|
||||
return know_end;
|
||||
}
|
||||
|
||||
cigar->n = cn;
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
||||
// ///p_length might be samller than t_length + 2 * errthold
|
||||
inline int32_t ed_band_cal_semi_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre,
|
||||
int32_t know_err, int32_t know_end, int32_t *r_err, int32_t *r_beg, Word *buf, asg16_v *cigar, int32_t *cigar_l) {
|
||||
int32_t cn = cigar->n; (*r_err) = (*r_beg) = INT32_MAX; (*cigar_l) = 0;
|
||||
Word Peq[5] = {0}, mm = (Word)1, VP = 0, VN = 0, X = 0, D0 = 0, HN = 0, HP = 0, i_col, i_col_dux;
|
||||
int32_t bd = (thre<<1)+1, i, err = 0, i_bd = (thre<<1), last_high = (thre<<1), tn0 = tn - 1;
|
||||
int32_t cut = thre+last_high; ///kv_resize(uint16_t, *cigar, cigar->n+(uint32_t)know_err+2);//pre-alloc
|
||||
|
||||
if(ungap_trace(pstr, pn, tstr, tn, know_err, know_end, r_err, r_beg, cigar, cigar_l) >= 0) {
|
||||
return know_end;
|
||||
}
|
||||
|
||||
for (i = 0; i < bd; i++) {
|
||||
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
|
||||
}
|
||||
Peq[4] = 0;
|
||||
///should make Peq[4] = 0 if N is always an error
|
||||
i = i_col = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char
|
||||
|
||||
while (i < tn0) {
|
||||
X = Peq[seq_nt4_table[(uint8_t)tstr[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&(1ULL))) {
|
||||
++err;
|
||||
if (err>cut) return -1;
|
||||
}
|
||||
|
||||
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1; ///Peq[4] >>= 1;
|
||||
|
||||
++i; ++i_bd;
|
||||
Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;
|
||||
|
||||
buf[i_col++] = D0; buf[i_col++] = VP; buf[i_col++] = VN; buf[i_col++] = HP; buf[i_col++] = HN;
|
||||
}
|
||||
|
||||
X = Peq[seq_nt4_table[(uint8_t)tstr[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&(1ULL))) {
|
||||
++err;
|
||||
if (err>cut) return -1;
|
||||
}
|
||||
|
||||
buf[i_col++] = D0; buf[i_col++] = VP; buf[i_col++] = VN; buf[i_col++] = HP; buf[i_col++] = HN;
|
||||
|
||||
i_col_dux = i_col/tn;
|
||||
|
||||
int32_t site = tn - 1, end = -1;///up bound
|
||||
///in most cases, ai = (thre<<1)
|
||||
int32_t ai = pn - tn, uge = INT32_MAX;
|
||||
if ((err <= thre) && (err<=(*r_err))) {
|
||||
*r_err = err; end = site;
|
||||
}
|
||||
i = 0;
|
||||
|
||||
while (i < ai) {
|
||||
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL)); ++i;
|
||||
if ((err <= thre) && (err <= (*r_err))) {
|
||||
*r_err = err; end = site + i;
|
||||
}
|
||||
if(i == thre) uge = err;
|
||||
}
|
||||
if((uge<=thre) && (uge == (*r_err))) end = site + thre;
|
||||
if ((*r_err) > thre) return end;
|
||||
|
||||
|
||||
///need to correct pn here, since pn might be smaller than tn + 2* thre
|
||||
pn = tn + (thre<<1);
|
||||
int32_t beg = end, back_track_site = bd - (pn - end);
|
||||
|
||||
Word v_value, h_value, delta_value, min_value, current_value;
|
||||
///Word direction; ///0 is match, 1 is mismatch, 2 is up, 3 is left
|
||||
Word direction = 0, *ba, pd, pdl; ///0 is match, 1 is mismatch, 2 is up, 3 is left
|
||||
i = tn; pd = (Word)-1; pdl = 0;
|
||||
current_value = *r_err;
|
||||
int32_t low_bound = bd - 1;
|
||||
|
||||
while (i > 0) {
|
||||
if (current_value == 0) break;
|
||||
ba = buf + ((i*i_col_dux) - i_col_dux);
|
||||
delta_value = current_value - ((~(ba[0]>>back_track_site))&(1ULL));
|
||||
|
||||
if (back_track_site == 0) {
|
||||
///HP
|
||||
h_value = current_value - ((ba[3] >> back_track_site)&(1ULL));
|
||||
//HN
|
||||
h_value = h_value + ((ba[4] >> back_track_site)&1ULL);
|
||||
min_value = delta_value; direction = 0;
|
||||
if (h_value < min_value) {
|
||||
min_value = h_value;
|
||||
direction = 3;
|
||||
}
|
||||
} else if (back_track_site == low_bound) {
|
||||
v_value = current_value - ((ba[1]>>(back_track_site-1))&(1ULL));
|
||||
v_value = v_value + ((ba[2]>>(back_track_site-1))&(1ULL));
|
||||
|
||||
min_value = delta_value; direction = 0;
|
||||
if (v_value < min_value) {
|
||||
min_value = v_value;
|
||||
direction = 2;
|
||||
}
|
||||
}
|
||||
else {
|
||||
h_value = current_value-((ba[3]>>back_track_site)&(1ULL));
|
||||
h_value = h_value+((ba[4]>>back_track_site)&(1ULL));
|
||||
|
||||
v_value = current_value - ((ba[1]>>(back_track_site-1))&(1ULL));
|
||||
v_value = v_value + ((ba[2]>>(back_track_site-1))&(1ULL));
|
||||
|
||||
min_value = delta_value; direction = 0;
|
||||
if (v_value < min_value) {
|
||||
min_value = v_value;
|
||||
direction = 2;
|
||||
}
|
||||
|
||||
if (h_value < min_value) {
|
||||
min_value = h_value;
|
||||
direction = 3;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if (direction == 0) {
|
||||
if (delta_value != current_value) {
|
||||
direction = 1;
|
||||
}
|
||||
i--; beg--;
|
||||
}
|
||||
if (direction == 2) {///ru guo xiang shang yi dong, bing bu huan lie
|
||||
back_track_site--; beg--;
|
||||
}
|
||||
else if (direction == 3) {///ru guo xiang zuo yi dong
|
||||
i--;
|
||||
back_track_site++;
|
||||
}
|
||||
|
||||
if(direction != pd) {
|
||||
if(pdl > 0) push_trace(cigar, pd, pdl);
|
||||
pd = direction; pdl = 1;
|
||||
} else {
|
||||
pdl++;
|
||||
}
|
||||
// path[path_length++] = direction;
|
||||
current_value = min_value;
|
||||
}
|
||||
|
||||
|
||||
if (i > 0) {
|
||||
direction = 0; beg -= i;
|
||||
if(direction != pd) {
|
||||
if(pdl > 0) push_trace(cigar, pd, pdl);
|
||||
pd = direction; pdl = i;
|
||||
} else {
|
||||
pdl += i;
|
||||
}
|
||||
}
|
||||
|
||||
if(pdl > 0) push_trace(cigar, pd, pdl);
|
||||
if (direction != 3) beg++;
|
||||
|
||||
uint16_t *trac = cigar->a + cn, tt; int32_t trac_n = cigar->n - cn; ai = trac_n>>1;
|
||||
for (i = 0; i < ai; i++) {
|
||||
tt = trac[i]; trac[i] = trac[trac_n-i-1]; trac[trac_n-i-1] = tt;
|
||||
}
|
||||
(*cigar_l) = cigar->n - cn;
|
||||
|
||||
(*r_beg) = beg; (*cigar_l) = cigar->n - cn;
|
||||
return end;
|
||||
}
|
||||
|
||||
|
||||
#endif
|
||||
|
||||
Reference in New Issue
Block a user