mirror of
https://github.com/chhylp123/hifiasm.git
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edit distance based error correction
This commit is contained in:
Haoyu Cheng
+685
@@ -0,0 +1,685 @@
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#include <stdio.h>
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#include <stdlib.h>
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#include <stdint.h>
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#include "Correct.h"
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#include "Levenshtein_distance.h"
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#include "edlib.h"
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long long T_total_match=0;
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long long T_total_unmatch=0;
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long long T_total_mis=0;
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#define MAX(x, y) ((x >= y)?x:y)
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#define MIN(x, y) ((x <= y)?x:y)
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#define OVERLAP(x_start, x_end, y_start, y_end) (MIN(x_end, y_end) - MAX(x_start, y_start) + 1)
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///#define OVERLAP(x_start, x_end, y_start, y_end) MIN(x_end, y_end) - MAX(x_start, y_start) + 1
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///y_length > x_length
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unsigned int edit_distance_normal_test_banded(char* y, int y_length, char* x, int x_length, int error_cut, int matrix[1000][1000] )
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{ memset(matrix, 0, sizeof(matrix));
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int i, j;
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for (i = 0; i <= x_length; i++)
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{
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matrix[i][0] = i;
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}
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int digonal, up, left;
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unsigned int min;
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///一列列算的
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for (i = 0; i < x_length; i++)
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{
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for (j = 0; j < y_length; j++)
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{
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///matrix[i + 1][j + 1]
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digonal = matrix[i][j] + (x[i] != y[j]);
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up = matrix[i + 1][j] + 1;
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left = matrix[i][j + 1] + 1;
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min = digonal;
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if (up < min)
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{
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min = up;
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}
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if (left< min)
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{
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min = left;
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}
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matrix[i + 1][j + 1] = min;
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}
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}
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min = (unsigned int)-1;
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for (j = x_length; j <= y_length; j++)
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{
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if (matrix[i][j] < min)
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{
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min = matrix[i][j];
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}
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}
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return min <= error_cut?min:(unsigned int)(-1);
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}
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void verify_get_interval(long long window_start, long long window_end, overlap_region_alloc* overlap_list,Correct_dumy* dumy)
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{
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long long i;
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long long match_length = 0;
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long long match_lengthNT = 0;
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long long Len;
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for (i = 0; i < overlap_list->length; i++)
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{
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if((Len = OVERLAP(window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e)) > 0)
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{
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if (Len == WINDOW)
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{
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match_length++;
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long long j;
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for (j = 0; j < dumy->length; j++)
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{
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if (i==dumy->overlapID[j])
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{
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break;
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}
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}
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if (j >= dumy->length)
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{
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fprintf(stderr, "+ERROR interval\n");
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fprintf(stderr, "i: %u, window_start: %u, window_end: %u, x_pos_s: %u, x_pos_e: %u\n",
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i, window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e);
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}
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}
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else
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{
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match_lengthNT++;
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long long j;
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for (j = 0; j < dumy->lengthNT; j++)
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{
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if (i==dumy->overlapID[dumy->size - j - 1])
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{
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break;
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}
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}
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if (j >= dumy->lengthNT)
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{
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fprintf(stderr, "-ERROR interval\n");
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fprintf(stderr, "i: %u, window_start: %u, window_end: %u, x_pos_s: %u, x_pos_e: %u, dumy->lengthNT: %u\n",
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i, window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e, dumy->lengthNT);
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}
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}
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}
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}
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if (match_length != dumy->length || match_lengthNT != dumy->lengthNT)
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{
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fprintf(stderr, "****************ERROR interval length*******************\n");
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fprintf(stderr, "match_length: %u\n", match_length);
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fprintf(stderr, "dumy->length: %u\n", dumy->length);
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fprintf(stderr, "window_start: %u, window_end: %u\n", window_start, window_end);
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}
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}
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inline int get_interval_back(long long window_start, long long window_end, overlap_region_alloc* overlap_list, Correct_dumy* dumy)
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{
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long long i;
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int flag = 0;
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for (i = dumy->start_i; i < overlap_list->length; i++)
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{
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///只会发生在这个interval比list里所有元素都小的情况
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///这种情况下一个interval需要从0开始
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if (window_start < overlap_list->list[i].x_pos_s)
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{
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dumy->start_i = 0;
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dumy->length = 0;
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return -1;
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}
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else if(window_start >= overlap_list->list[i].x_pos_s && window_start <= overlap_list->list[i].x_pos_e)
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{
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dumy->start_i = i;
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break;
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}
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}
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///只会发生在这个window比list里所有元素都大的情况
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///这种情况下一个window也无需遍历了
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if (i >= overlap_list->length)
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{
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dumy->start_i = overlap_list->length;
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dumy->length = 0;
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return -2;
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}
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///走到这里的时候，至少window_start的要求是满足了
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dumy->length = 0;
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for (; i < overlap_list->length; i++)
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{
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if(overlap_list->list[i].x_pos_s <= window_start && overlap_list->list[i].x_pos_e >= window_end)
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{
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dumy->overlapID[dumy->length] = i;
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dumy->length++;
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}
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else if(overlap_list->list[i].x_pos_s > window_start)
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{
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break;
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}
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}
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if ( dumy->length == 0)
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{
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return 0;
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}
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else
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{
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return 1;
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}
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}
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inline int get_interval(long long window_start, long long window_end, overlap_region_alloc* overlap_list, Correct_dumy* dumy)
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{
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long long i;
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int flag = 0;
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long long Begin, End, Len;
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for (i = dumy->start_i; i < overlap_list->length; i++)
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{
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///只会发生在这个interval比list里所有元素都小的情况
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///这种情况下一个interval需要从0开始
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if (window_end < overlap_list->list[i].x_pos_s)
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{
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dumy->start_i = 0;
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dumy->length = 0;
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return 0;
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}
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else ///只要window_end >= overlap_list->list[i].x_pos_s，就有可能重叠
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{
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dumy->start_i = i;
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break;
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}
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}
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///只会发生在这个window比list里所有元素都大的情况
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///这种情况下一个window也无需遍历了
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if (i >= overlap_list->length)
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{
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dumy->start_i = overlap_list->length;
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dumy->length = 0;
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return -2;
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}
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dumy->length = 0;
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dumy->lengthNT = 0;
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for (; i < overlap_list->length; i++)
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{
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if((Len = OVERLAP(window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e)) > 0)
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{
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if (Len == WINDOW)
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{
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dumy->overlapID[dumy->length] = i;
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dumy->length++;
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}
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else
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{
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dumy->lengthNT++;
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dumy->overlapID[dumy->size - dumy->lengthNT] = i;
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}
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}
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if(overlap_list->list[i].x_pos_s > window_end)
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{
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break;
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}
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}
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if ( dumy->length + dumy->lengthNT == 0)
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{
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return 0;
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}
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else
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{
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return 1;
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}
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}
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///Len = OVERLAP(window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e))
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void print_string(char* s, int l)
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{
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for (size_t i = 0; i < l; i++)
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{
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fprintf(stderr, "%c", s[i]);
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}
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fprintf(stderr, "\n");
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}
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void test_edit_distance_by_edlib(char* x_string, char* y_string, long long x_len,
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long long o_len, int threashold, int error, long long* total_mis)
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{
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EdlibAlignResult result = edlibAlign(x_string, x_len, y_string, o_len,
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edlibNewAlignConfig(threashold, EDLIB_MODE_HW, EDLIB_TASK_PATH, NULL, 0));
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if (result.status == EDLIB_STATUS_OK) {
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if (result.editDistance != error)
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///if (result.editDistance != error && result.endLocations[0] > x_len)
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{
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(*total_mis)++;
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if ((int)error != -1 && result.editDistance==-1)
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{
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fprintf(stderr, "ERROR1\n");
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}
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if ((int)error < result.editDistance==-1 &&
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(int)error != -1 && result.editDistance!=-1)
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{
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fprintf(stderr, "ERROR2\n");
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}
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int up_length = o_len - result.endLocations[0] - 1;
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int left_length = result.endLocations[0] - x_len;
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char* cigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, EDLIB_CIGAR_STANDARD);
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int cigar_length = strlen(cigar);
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/**
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for (int i = cigar_length - 1; i >= 0; i--)
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{
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switch (cigar[i])
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{
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case 'I':
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break;
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default:
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break;
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}
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}
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**/
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///fprintf(stderr,"%s\n", cigar);
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free(cigar);
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/**
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fprintf(stderr, "****\ni: %u, edlib: %d, alignmentLength: %d, startLocations: %d, endLocations: %d\n",
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i, result.editDistance, result.alignmentLength, result.startLocations[0], result.endLocations[0]);
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char* cigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, EDLIB_CIGAR_STANDARD);
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fprintf(stderr,"%s\n", cigar);
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free(cigar);
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print_string(x_string, x_len);
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print_string(y_string, o_len);
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fprintf(stderr, "BPM: %d\n", error);
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**/
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}
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}
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edlibFreeAlignResult(result);
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}
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void verify_window(long long window_start, long long window_end, overlap_region_alloc* overlap_list,Correct_dumy* dumy, All_reads* R_INF,
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char* r_string)
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{
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long long i;
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long long currentID, currentIDLen;
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long long x_start, y_start, o_len;
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long long Window_Len = WINDOW + (THRESHOLD << 1);
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char* x_string = NULL;
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char* y_string = NULL;
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long long x_end, x_len;
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int end_site;
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unsigned int error;
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long long total_match=0;
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long long total_unmatch=0;
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long long total_mis=0;
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///这些是整个window被完全覆盖的
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for (i = 0; i < dumy->length; i++)
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{
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///整个window被覆盖的话，read本身上的区间就是[window_start, window_end]
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x_len = WINDOW;
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currentID = dumy->overlapID[i];
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x_start = window_start;
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///y上的相对位置
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y_start = (x_start - overlap_list->list[currentID].x_pos_s) + overlap_list->list[currentID].y_pos_s;
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///y上的起始
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y_start = y_start - THRESHOLD;
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if (y_start < 0)
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{
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y_start = 0;
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}
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///当前y的长度
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currentIDLen = Get_READ_LENGTH((*R_INF), overlap_list->list[currentID].y_id);
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///不能超过y的剩余长度
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o_len = MIN(Window_Len, currentIDLen - y_start);
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recover_UC_Read_sub_region(dumy->overlap_region, y_start, o_len, overlap_list->list[currentID].y_pos_strand,
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R_INF, overlap_list->list[currentID].y_id);
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x_string = r_string + x_start;
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y_string = dumy->overlap_region;
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///这个长度足够，可以用来一起比
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if (Window_Len == o_len)
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{
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end_site = Reserve_Banded_BPM(y_string, o_len, x_string, x_len, THRESHOLD, &error);
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if (error!=(unsigned int)-1)
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{
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total_match++;
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}
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else
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{
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total_unmatch++;
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}
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test_edit_distance_by_edlib(x_string, y_string, x_len,
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o_len, THRESHOLD, error, &total_mis);
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}
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else ///这个不够，只能单个比 ///不够的地方要置N
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{
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/**
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end_site = Reserve_Banded_BPM(y_string, o_len, x_string, x_len, THRESHOLD, &error);
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if (error!=-1)
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{
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total_match++;
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}
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else
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{
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total_unmatch++;
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}
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**/
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}
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}
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long long reverse_i = dumy->size - 1;
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///这些是整个window被部分覆盖的
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for (i = 0; i < dumy->lengthNT; i++)
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{
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currentID = dumy->overlapID[reverse_i--];
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x_start = MAX(window_start, overlap_list->list[currentID].x_pos_s);
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x_end = MIN(window_end, overlap_list->list[currentID].x_pos_e);
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///这个是和当前窗口重叠的长度
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x_len = x_end - x_start + 1;
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if (x_len <= 0)
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{
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fprintf(stderr, "ERROR\n");
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}
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///y上的相对位置
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y_start = (x_start - overlap_list->list[currentID].x_pos_s) + overlap_list->list[currentID].y_pos_s;
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///y上的起始
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y_start = y_start - THRESHOLD;
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if (y_start < 0)
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{
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y_start = 0;
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}
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///当前y的长度
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currentIDLen = Get_READ_LENGTH((*R_INF), overlap_list->list[currentID].y_id);
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///不能超过y的剩余长度
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Window_Len = x_len + (THRESHOLD << 1);
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o_len = MIN(Window_Len, currentIDLen - y_start);
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recover_UC_Read_sub_region(dumy->overlap_region, y_start, o_len, overlap_list->list[currentID].y_pos_strand,
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R_INF, overlap_list->list[currentID].y_id);
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x_string = r_string + x_start;
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y_string = dumy->overlap_region;
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///不够的地方要置N
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end_site = Reserve_Banded_BPM(y_string, o_len, x_string, x_len, THRESHOLD, &error);
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/**
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if (error!=-1)
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{
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total_match++;
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}
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else
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{
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total_unmatch++;
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}
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**/
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}
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/**
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if (total_match!=0)
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{
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||||
fprintf(stderr, "total_match: %u\n", total_match);
|
||||
fprintf(stderr, "total_unmatch: %u\n", total_unmatch);
|
||||
fprintf(stderr, "total_mis: %u\n", total_mis);
|
||||
|
||||
}
|
||||
**/
|
||||
|
||||
T_total_match = T_total_match + total_match;
|
||||
T_total_unmatch = T_total_unmatch + total_unmatch;
|
||||
T_total_mis = T_total_mis + total_mis;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Read* g_read, Correct_dumy* dumy)
|
||||
{
|
||||
reverse_complement(g_read->seq, g_read->length);
|
||||
|
||||
clear_Correct_dumy(dumy, overlap_list);
|
||||
|
||||
long long window_num = (g_read->length + WINDOW - 1) / WINDOW;
|
||||
|
||||
long long i;
|
||||
|
||||
long long window_start, window_end;
|
||||
|
||||
window_start = 0;
|
||||
window_end = WINDOW - 1;
|
||||
|
||||
|
||||
|
||||
/**
|
||||
UC_Read debug_read;
|
||||
init_UC_Read(&debug_read);
|
||||
|
||||
for (i = 0; i < overlap_list->length; i++)
|
||||
{
|
||||
|
||||
if (overlap_list->list[i].y_pos_strand)
|
||||
{
|
||||
recover_UC_Read_RC(&debug_read, R_INF, overlap_list->list[i].y_id);
|
||||
}
|
||||
else
|
||||
{
|
||||
recover_UC_Read(&debug_read, R_INF, overlap_list->list[i].y_id);
|
||||
}
|
||||
|
||||
|
||||
long long x_length = overlap_list->list[i].x_pos_e - overlap_list->list[i].x_pos_s + 1;
|
||||
long long y_length = overlap_list->list[i].y_pos_e - overlap_list->list[i].y_pos_s + 1;
|
||||
|
||||
EdlibAlignResult result = edlibAlign(g_read->seq+overlap_list->list[i].x_pos_s,
|
||||
x_length,
|
||||
debug_read.seq + overlap_list->list[i].y_pos_s,
|
||||
y_length,
|
||||
edlibNewAlignConfig(-1, EDLIB_MODE_NW, EDLIB_TASK_DISTANCE, NULL, 0));
|
||||
|
||||
|
||||
if (result.status == EDLIB_STATUS_OK) {
|
||||
if (result.editDistance>0 && result.editDistance < x_length*0.02)
|
||||
{
|
||||
fprintf(stderr, "inner_i: %u, x_length: %u, y_length: %u, editDistance: %u\n",
|
||||
i, x_length, y_length, result.editDistance);
|
||||
fprintf(stderr, "x_pos_s: %u, x_pos_e: %u\n",
|
||||
overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e);
|
||||
fprintf(stderr, "y_pos_s: %u, y_pos_e: %u, y_pos_strand: %u\n",
|
||||
overlap_list->list[i].y_pos_s, overlap_list->list[i].y_pos_e, overlap_list->list[i].y_pos_strand);
|
||||
|
||||
|
||||
EdlibAlignResult n_result = edlibAlign(g_read->seq+overlap_list->list[i].x_pos_s,
|
||||
350,
|
||||
debug_read.seq + overlap_list->list[i].y_pos_s - 15,
|
||||
380,
|
||||
edlibNewAlignConfig(-1, EDLIB_MODE_HW, EDLIB_TASK_DISTANCE, NULL, 0));
|
||||
|
||||
fprintf(stderr, "n_editDistance: %u\n",
|
||||
n_result.editDistance);
|
||||
|
||||
|
||||
|
||||
|
||||
edlibFreeAlignResult(n_result);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
edlibFreeAlignResult(result);
|
||||
|
||||
|
||||
}
|
||||
|
||||
destory_UC_Read(&debug_read);
|
||||
**/
|
||||
///return;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
int flag;
|
||||
|
||||
for (i = 0; i < window_num; i++)
|
||||
{
|
||||
|
||||
dumy->length = 0;
|
||||
dumy->lengthNT = 0;
|
||||
flag = get_interval(window_start, window_end, overlap_list, dumy);
|
||||
|
||||
switch (flag)
|
||||
{
|
||||
case 1: ///找到匹配
|
||||
break;
|
||||
case 0: ///没找到匹配
|
||||
break;
|
||||
case -2: ///下一个window也不会存在匹配, 直接跳出
|
||||
i = window_num;
|
||||
break;
|
||||
}
|
||||
|
||||
if(dumy->length + dumy->lengthNT>overlap_list->length)
|
||||
{
|
||||
fprintf(stderr, "error length\n");
|
||||
}
|
||||
|
||||
///verify_get_interval(window_start, window_end, overlap_list, dumy);
|
||||
|
||||
verify_window(window_start, window_end, overlap_list, dumy, R_INF, g_read->seq);
|
||||
|
||||
window_start = window_start + WINDOW;
|
||||
window_end = window_end + WINDOW;
|
||||
if (window_end >= g_read->length)
|
||||
{
|
||||
window_end = g_read->length - 1;
|
||||
}
|
||||
|
||||
///break;
|
||||
|
||||
}
|
||||
|
||||
|
||||
fprintf(stderr, "total_match: %u, total_unmatch: %u, total_mis: %u\n",
|
||||
T_total_match, T_total_unmatch, T_total_mis);
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
void init_Correct_dumy(Correct_dumy* list)
|
||||
{
|
||||
list->size = 0;
|
||||
list->length = 0;
|
||||
list->lengthNT = 0;
|
||||
list->start_i = 0;
|
||||
list->overlapID = NULL;
|
||||
}
|
||||
|
||||
void destory_Correct_dumy(Correct_dumy* list)
|
||||
{
|
||||
free(list->overlapID);
|
||||
}
|
||||
|
||||
void clear_Correct_dumy(Correct_dumy* list, overlap_region_alloc* overlap_list)
|
||||
{
|
||||
list->length = 0;
|
||||
list->lengthNT = 0;
|
||||
list->start_i = 0;
|
||||
|
||||
if (list->size < overlap_list->length)
|
||||
{
|
||||
list->size = overlap_list->length;
|
||||
list->overlapID = (uint64_t*)realloc(list->overlapID, list->size*sizeof(uint64_t));
|
||||
}
|
||||
|
||||
}
|
||||
Reference in New Issue
Block a user