#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <pthread.h>
#include "Correct.h"
#include "Levenshtein_distance.h"
#include "edlib.h"

long long T_total_match=0;
long long T_total_unmatch=0;
long long T_total_mis=0;
pthread_mutex_t debug_statistics ;






///y_length > x_length
unsigned int edit_distance_normal_test_banded(char* y, int y_length, char* x, int x_length, int error_cut, int matrix[1000][1000] )
{   memset(matrix, 0, sizeof(matrix));

    int i, j;
    for (i = 0; i <= x_length; i++)
    {
        matrix[i][0] = i;
    }

    int digonal, up, left;
    unsigned int min;

    ///一列列算的
    for (i = 0; i < x_length; i++)
    {
        for (j = 0; j < y_length; j++)
        {
            ///matrix[i + 1][j + 1]
            digonal = matrix[i][j] + (x[i] !=  y[j]);
            up = matrix[i + 1][j] + 1;
            left = matrix[i][j + 1] + 1;
            min = digonal;
            if (up < min)
            {
                min = up;
            }

            if (left< min)
            {
                min = left;
            }

            matrix[i + 1][j + 1] = min;
        }
    }

    min = (unsigned int)-1;
    for (j = x_length; j <= y_length; j++)
    {
        if (matrix[i][j] < min)
        {
            min = matrix[i][j];
        }
    }


    return min <= error_cut?min:(unsigned int)(-1);
}

void verify_get_interval(long long window_start, long long window_end, overlap_region_alloc* overlap_list,Correct_dumy* dumy)
{
    long long i;
    long long match_length = 0;
    long long match_lengthNT = 0;
    long long Len;

    for (i = 0; i < overlap_list->length; i++)
    {
        if((Len = OVERLAP(window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e)) > 0)
        {
            if (Len == WINDOW)
            {
                match_length++;
                long long j;
                for (j = 0; j < dumy->length; j++)
                {
                    if (i==dumy->overlapID[j])
                    {
                        break;
                    }
                }

                if (j >= dumy->length)
                {
                    fprintf(stderr, "+ERROR interval\n");
                
                    fprintf(stderr, "i: %u, window_start: %u, window_end: %u, x_pos_s: %u, x_pos_e: %u\n", 
                    i, window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e);
                }
            }
            else
            {
                match_lengthNT++;
                long long j;
                for (j = 0; j < dumy->lengthNT; j++)
                {
                    if (i==dumy->overlapID[dumy->size - j - 1])
                    {
                        break;
                    }
                }

                if (j >= dumy->lengthNT)
                {
                    fprintf(stderr, "-ERROR interval\n");
                
                    fprintf(stderr, "i: %u, window_start: %u, window_end: %u, x_pos_s: %u, x_pos_e: %u, dumy->lengthNT: %u\n", 
                    i, window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e, dumy->lengthNT);
                }
            }
            
            

           
        
        }
    }

    if (match_length != dumy->length || match_lengthNT != dumy->lengthNT)
    {
        fprintf(stderr, "****************ERROR interval length*******************\n");
        fprintf(stderr, "match_length: %u\n", match_length);
        fprintf(stderr, "dumy->length: %u\n", dumy->length);
        fprintf(stderr, "window_start: %u, window_end: %u\n", window_start, window_end);
    }
    
}


inline int get_interval_back(long long window_start, long long window_end, overlap_region_alloc* overlap_list, Correct_dumy* dumy)
{
    long long i;
    int flag = 0;

    for (i = dumy->start_i; i < overlap_list->length; i++)
    {
        ///只会发生在这个interval比list里所有元素都小的情况
        ///这种情况下一个interval需要从0开始
        if (window_start < overlap_list->list[i].x_pos_s)
        {
            dumy->start_i = 0;
            dumy->length = 0;
            return -1;
        }
        else if(window_start >= overlap_list->list[i].x_pos_s && window_start <= overlap_list->list[i].x_pos_e)
        {
            dumy->start_i = i;
            break;
        }
    }

    ///只会发生在这个window比list里所有元素都大的情况
    ///这种情况下一个window也无需遍历了
    if (i >= overlap_list->length)
    {
        dumy->start_i = overlap_list->length;
        dumy->length = 0;
        return -2;
    }
    
    ///走到这里的时候，至少window_start的要求是满足了
    dumy->length = 0;

    for (; i < overlap_list->length; i++)
    {
        if(overlap_list->list[i].x_pos_s <= window_start && overlap_list->list[i].x_pos_e >= window_end)
        {
            dumy->overlapID[dumy->length] = i;
            dumy->length++;
        }
        else if(overlap_list->list[i].x_pos_s > window_start)
        {
            break;
        }
    }

    if ( dumy->length == 0)
    {
        return 0;
    }
    else
    {
        return 1;
    }
}



inline int get_interval(long long window_start, long long window_end, overlap_region_alloc* overlap_list, Correct_dumy* dumy)
{
    long long i;
    int flag = 0;
    long long Begin, End, Len;


    for (i = dumy->start_i; i < overlap_list->length; i++)
    {
        ///只会发生在这个interval比list里所有元素都小的情况
        ///这种情况下一个interval需要从0开始
        if (window_end < overlap_list->list[i].x_pos_s)
        {
            dumy->start_i = 0;
            dumy->length = 0;
            return 0;
        }
        else ///只要window_end >= overlap_list->list[i].x_pos_s，就有可能重叠
        {
            dumy->start_i = i;
            break;
        }
    }

    ///只会发生在这个window比list里所有元素都大的情况
    ///这种情况下一个window也无需遍历了
    if (i >= overlap_list->length)
    {
        dumy->start_i = overlap_list->length;
        dumy->length = 0;
        return -2;
    }
    
    dumy->length = 0;
    dumy->lengthNT = 0;

    for (; i < overlap_list->length; i++)
    {
        
        if((Len = OVERLAP(window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e)) > 0)
        {
            if (Len == WINDOW)
            {
                dumy->overlapID[dumy->length] = i;
                dumy->length++; 
            }
            else
            {
                dumy->lengthNT++;
                dumy->overlapID[dumy->size - dumy->lengthNT] = i;
            }
        }
        
        if(overlap_list->list[i].x_pos_s > window_end)
        {
            break;
        }
    }

    if ( dumy->length + dumy->lengthNT == 0)
    {
        return 0;
    }
    else
    {
        return 1;
    }
}

///Len = OVERLAP(window_start, window_end, overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e))

void print_string(char* s, int l)
{
    for (size_t i = 0; i < l; i++)
    {
        fprintf(stderr, "%c", s[i]);
    }

    fprintf(stderr, "\n");
    
}

void test_edit_distance_by_edlib(char* x_string, char* y_string, long long x_len, 
long long o_len, int threashold, int error, long long* total_mis)
{
    EdlibAlignResult result = edlibAlign(x_string, x_len, y_string, o_len, 
    edlibNewAlignConfig(threashold, EDLIB_MODE_HW, EDLIB_TASK_PATH, NULL, 0));

    if (result.status == EDLIB_STATUS_OK) {
        if (result.editDistance != error)
        {   
            
            (*total_mis)++;


            if ((int)error != -1 && result.editDistance==-1)
            {
                fprintf(stderr, "ERROR1\n");
            }

            if ((int)error < result.editDistance==-1 && 
            (int)error != -1 && result.editDistance!=-1)
            {
                fprintf(stderr, "ERROR2\n");
            }

            int up_length = o_len - result.endLocations[0] - 1;
            int left_length = result.endLocations[0] - x_len;

            
            char* cigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, EDLIB_CIGAR_STANDARD);
            int cigar_length = strlen(cigar);

            int i = cigar_length - 1;
            int j = 0;
            char tmp;
           

            while (i >= 0)
            {
                if (up_length < 0 || left_length < 0)
                {
                    break;
                }

                if (cigar[i] == 'I' || cigar[i] == 'D')
                {
                    tmp = cigar[i];
                    cigar[i] = '\0';
                    j = i - 1;
                    while (cigar[j] <= '9' && cigar[j] >= '0' && j >= 0)
                    {
                        j--;
                    }
                    j++;
                    int Len = atoi(cigar + j);
                    cigar[i] = tmp;
                    i = j - 1;

                    if (tmp == 'I')
                    {
                        up_length = up_length - Len;
                        left_length = left_length + Len;
                    }
                    else
                    {
                        left_length = left_length - Len;
                        up_length = up_length + Len;
                    }
                }
                else
                {
                    i--;
                }
            }

            
            if (up_length >= 0 && left_length >= 0)
            {
                fprintf(stderr, "****\nedlib: %d, alignmentLength: %d, startLocations: %d, endLocations: %d\n", 
                result.editDistance, result.alignmentLength, result.startLocations[0], result.endLocations[0]);
                fprintf(stderr,"%s\n", cigar);
                print_string(x_string, x_len);
                print_string(y_string, o_len);
                fprintf(stderr, "BPM: %d\n", error);
            }

            free(cigar);
        }
    }
    edlibFreeAlignResult(result);
}

void verify_window(long long window_start, long long window_end, overlap_region_alloc* overlap_list,Correct_dumy* dumy, All_reads* R_INF,
char* r_string)
{

    long long i;
    long long currentID, currentIDLen;
    long long x_start, y_start, o_len;
    long long Window_Len = WINDOW + (THRESHOLD << 1);
    char* x_string = NULL;
    char* y_string = NULL;
    long long x_end, x_len;
    int end_site;
    unsigned int error;
    /************需要注释掉********* */ 
    // long long total_match=0;
    // long long total_unmatch=0;
    // long long total_mis=0;
    /************需要注释掉********* */
    int groupLen = 0;
    int return_sites[GROUP_SIZE];
	unsigned int return_sites_error[GROUP_SIZE];
    uint64_t overlapID[GROUP_SIZE];

    ///这些是整个window被完全覆盖的
    for (i = 0; i < dumy->length; i++)
    {
        ///整个window被覆盖的话，read本身上的区间就是[window_start, window_end]
        x_len = WINDOW;
        currentID = dumy->overlapID[i];
        x_start = window_start;
        ///y上的相对位置
        y_start = (x_start - overlap_list->list[currentID].x_pos_s) + overlap_list->list[currentID].y_pos_s;

        // /************需要注释掉**********/
        // if(x_start < overlap_list->list[currentID].x_pos_s)
        // {
        //     fprintf(stderr, "ERROR\n");
        // }
        // /************需要注释掉**********/
        ///y上的起始
        y_start = y_start - THRESHOLD;
        if (y_start < 0)
        {
            y_start = 0;
        }
        ///当前y的长度
        currentIDLen = Get_READ_LENGTH((*R_INF), overlap_list->list[currentID].y_id);
        ///不能超过y的剩余长度
        o_len = MIN(Window_Len, currentIDLen - y_start);

        // /************需要注释掉**********/
        // if(o_len < x_len)
        // {
        //     fprintf(stderr, "ERROR\n");
        // }
        // /************需要注释掉**********/
        
        
        ///这个长度足够，可以用来一起比
        if (Window_Len == o_len)
        {

            recover_UC_Read_sub_region(dumy->overlap_region_group[groupLen], y_start, o_len, overlap_list->list[currentID].y_pos_strand, 
                R_INF, overlap_list->list[currentID].y_id);
            
            overlapID[groupLen] = currentID;

            x_string = r_string + x_start;

            groupLen++;
            if (groupLen == GROUP_SIZE)
            {
            
                Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1], 
                dumy->overlap_region_group[2], dumy->overlap_region_group[3], o_len, x_string, x_len,
			        return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
                groupLen = 0;

                if (return_sites_error[0]!=(unsigned int)-1)
                {
                    overlap_list->list[overlapID[0]].align_length += x_len;
                }

                if (return_sites_error[1]!=(unsigned int)-1)
                {
                    overlap_list->list[overlapID[1]].align_length += x_len;
                }

                if (return_sites_error[2]!=(unsigned int)-1)
                {
                    overlap_list->list[overlapID[2]].align_length += x_len;
                }

                if (return_sites_error[3]!=(unsigned int)-1)
                {
                    overlap_list->list[overlapID[3]].align_length += x_len;
                }

                
               
               /************需要注释掉**********/
            //    for (size_t ijk = 0; ijk < GROUP_SIZE; ijk++)
            //    {
            //        if (return_sites_error[ijk]!=(unsigned int)-1)
            //         {
            //             total_match++;
            //         }
            //         else
            //         {
            //             total_unmatch++;
            //         }
            //         test_edit_distance_by_edlib(x_string, dumy->overlap_region_group[ijk], x_len, o_len, THRESHOLD, 
            //         return_sites_error[ijk], &total_mis);
            //    }
                /************需要注释掉********* */
                
            }

        }
        else  ///这个不够，只能单个比 ///不够的地方要置N
        {

            recover_UC_Read_sub_region(dumy->overlap_region, y_start, o_len, overlap_list->list[currentID].y_pos_strand, 
                R_INF, overlap_list->list[currentID].y_id);

            x_string = r_string + x_start;
            y_string = dumy->overlap_region;

            ///o_len < Window_Len, 说明y的长度不够，需要在y后面补N
            memset (y_string + o_len, 0, Window_Len - o_len);
            end_site = Reserve_Banded_BPM(y_string, o_len, x_string, x_len, THRESHOLD, &error);


            if (error!=(unsigned int)-1)
            {
                overlap_list->list[currentID].align_length += x_len;
            }
            
            /************需要注释掉**********/
            // if (error!=(unsigned int)-1)
            // {
            //     total_match++;
            // }
            // else
            // {
            //     total_unmatch++;
            // }
            // test_edit_distance_by_edlib(x_string, y_string, x_len, o_len, THRESHOLD, error, &total_mis);
            /************需要注释掉********* */
        }
    }



    if (groupLen == 1)
    {
        end_site = Reserve_Banded_BPM(dumy->overlap_region_group[0], o_len, x_string, x_len, THRESHOLD, &error);

        if (error!=(unsigned int)-1)
        {
            overlap_list->list[overlapID[0]].align_length += x_len;
        }

        /************需要注释掉**********/
        // if (error!=(unsigned int)-1)
        // {
        //     total_match++;
        // }
        // else
        // {
        //     total_unmatch++;
        // }
        // test_edit_distance_by_edlib(x_string, dumy->overlap_region_group[0], x_len, o_len, THRESHOLD, error, &total_mis);
        /************需要注释掉********* */
    }
    else if (groupLen > 1)
    {
        Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1], 
                dumy->overlap_region_group[2], dumy->overlap_region_group[3], o_len, x_string, x_len,
			        return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);

        for (i = 0; i < groupLen; i++)
        {
            if (return_sites_error[i]!=(unsigned int)-1)
            {
                overlap_list->list[overlapID[i]].align_length += x_len;
            }
        }
        /************需要注释掉**********/
        // for (size_t ijk = 0; ijk < groupLen; ijk++)
        // {
        //     if (return_sites_error[ijk]!=(unsigned int)-1)
        //     {
        //         total_match++;
        //     }
        //     else
        //     {
        //         total_unmatch++;
        //     }
        //     test_edit_distance_by_edlib(x_string, dumy->overlap_region_group[ijk], x_len, o_len, THRESHOLD, 
        //     return_sites_error[ijk], &total_mis);
        // }
        /************需要注释掉**********/
        groupLen = 0;
    }
    
    

    long long reverse_i = dumy->size - 1;
    
    ///这些是整个window被部分覆盖的
    for (i = 0; i < dumy->lengthNT; i++)
    {
        currentID = dumy->overlapID[reverse_i--];
        x_start = MAX(window_start, overlap_list->list[currentID].x_pos_s);
        x_end = MIN(window_end, overlap_list->list[currentID].x_pos_e);
        ///这个是和当前窗口重叠的长度
        x_len = x_end - x_start + 1;

        // /************需要注释掉**********/
        // if (x_len <= 0)
        // {
        //     fprintf(stderr, "ERROR\n");
        // }
        // /************需要注释掉**********/

        ///y上的相对位置
        y_start = (x_start - overlap_list->list[currentID].x_pos_s) + overlap_list->list[currentID].y_pos_s;

        // /************需要注释掉**********/
        // if(x_start < overlap_list->list[currentID].x_pos_s)
        // {
        //     fprintf(stderr, "ERROR\n");
        // }
        // /************需要注释掉**********/

        ///y上的起始
        y_start = y_start - THRESHOLD;
        if (y_start < 0)
        {
            y_start = 0;
        }
        
        ///当前y的长度
        currentIDLen = Get_READ_LENGTH((*R_INF), overlap_list->list[currentID].y_id);

        
        ///不能超过y的剩余长度
        Window_Len = x_len + (THRESHOLD << 1);
        o_len = MIN(Window_Len, currentIDLen - y_start);


        // /************需要注释掉**********/
        // if(o_len < x_len)
        // {
        //     fprintf(stderr, "ERROR\n");
        // }
        // /************需要注释掉**********/

        
        recover_UC_Read_sub_region(dumy->overlap_region, y_start, o_len, overlap_list->list[currentID].y_pos_strand, 
                R_INF, overlap_list->list[currentID].y_id);

        x_string = r_string + x_start;
        y_string = dumy->overlap_region;

        ///不够的地方要置N
        if (Window_Len != o_len)
        {
            ///o_len < Window_Len, 说明y的长度不够，需要在y后面补N
            memset (y_string + o_len, 0, Window_Len - o_len);
        }
        end_site = Reserve_Banded_BPM(y_string, o_len, x_string, x_len, THRESHOLD, &error);

        if (error!=(unsigned int)-1)
        {
            overlap_list->list[currentID].align_length += x_len;
        }


        /************需要注释掉********* */
        // if (error!=(unsigned int)-1)
        // {
        //     total_match++;
        // }
        // else
        // {
        //     total_unmatch++;
        // }
        // test_edit_distance_by_edlib(x_string, y_string, x_len, o_len, THRESHOLD, error, &total_mis);
        /************需要注释掉********* */
    }
    



    /************需要注释掉********* */
    // pthread_mutex_lock(&debug_statistics);
    // T_total_match = T_total_match + total_match;
    // T_total_unmatch = T_total_unmatch + total_unmatch;
    // T_total_mis = T_total_mis + total_mis;
	// pthread_mutex_unlock(&debug_statistics);
    /************需要注释掉********* */
        
}

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;
    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;
        }
    }


    
    /************需要注释掉********* */
    // pthread_mutex_lock(&debug_statistics);
    // fprintf(stderr, "total_match: %u, total_unmatch: %u, total_mis: %u\n", 
    // T_total_match, T_total_unmatch, T_total_mis);
	// pthread_mutex_unlock(&debug_statistics);
    /************需要注释掉********* */
}


void init_Correct_dumy(Correct_dumy* list)
{
    list->size = 0;
    list->length = 0;
    list->lengthNT = 0;
    list->start_i = 0;
    list->overlapID = NULL;
    int i;
    for (i = 0; i < 256; i++)
	{
		list->Peq_SSE[i] = _mm_setzero_si128();
	}
}

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));
    }
    
}


void pre_filter_by_nearby_single(k_mer_pos* new_n_list, k_mer_pos* old_n_list, uint64_t n_length, uint64_t n_end_pos, UC_Read* g_read, 
All_reads* R_INF, Correct_dumy* dumy, uint64_t* new_n_length)
{
    (*new_n_length) = 0;
    ///这种就是0，new_n_list也不需要有数据
    if (n_length == 0)
    {
        return;
    }
    
    char* x_string = NULL;
    char* y_string = NULL;
    

    long long  x_offset = (long long)(n_end_pos) - WINDOW + 1;
    if (x_offset < 0)
    {
        x_offset = 0;
    }

    ///x_length是x上待验证区间的实际长度
    ///x_offset是x上待验证区间的起始位置
    ///如果是向前取待验证区间，那么x_length至少大于等于40 (compressed k-mer长度，不是实际长度)
    long long x_length = n_end_pos - x_offset + 1;
    ///这种也不要过滤了，直接把old_n_list全部赋值过来就好了
    if (x_length < (WINDOW/2))
    {
        (*new_n_length) = n_length;
        memcpy(new_n_list, old_n_list, sizeof(k_mer_pos)*n_length);
        return;
    }
    long long Window_Len = x_length + (THRESHOLD << 1);
    x_string = g_read->seq + x_offset;


    long long y_offset;
    long long y_length;

    long long i = 0;

    long long y_read_length;
    int end_site;
    unsigned int error;

    for (i = 0; i < n_length; i++)
    {
        ////old_n_list[i].offset是y上k-mer的结束位置
        ///n_end_pos是x上k-mer的结束位置
        ///x_length是x上区间长度
        y_offset = (long long)(old_n_list[i].offset) - x_length;
        ///这种情况下弃疗
        if (y_offset < 0)
        {
            new_n_list[(*new_n_length)].readID = old_n_list[i].readID;
            new_n_list[(*new_n_length)].offset = old_n_list[i].offset;
            (*new_n_length)++;
            continue;
        }

        y_offset = y_offset - THRESHOLD;
        ///还能抢救
        if (y_offset < 0)
        {
            y_offset = 0;
        }

        ///y的read的总长度
        y_read_length = Get_READ_LENGTH((*R_INF), old_n_list[i].readID);
        y_length = MIN(Window_Len, y_read_length - y_offset);

        ///如果y的长度比x长度还小，那就直接弃疗了
        if (y_length < x_length)
        {
            new_n_list[(*new_n_length)].readID = old_n_list[i].readID;
            new_n_list[(*new_n_length)].offset = old_n_list[i].offset;
            (*new_n_length)++;
            continue;
        }
        
        ///y的方向都是0，因为索引里都是0
        recover_UC_Read_sub_region(dumy->overlap_region, y_offset, y_length, 0, R_INF, old_n_list[i].readID);
        y_string = dumy->overlap_region;

        memset (y_string + y_length, 0, Window_Len - y_length);
        end_site = Reserve_Banded_BPM(y_string, y_length, x_string, x_length, THRESHOLD, &error);

        if (error!=(unsigned int)-1)
        {
            new_n_list[(*new_n_length)].readID = old_n_list[i].readID;
            new_n_list[(*new_n_length)].offset = old_n_list[i].offset;
            (*new_n_length)++;
        }  
    }
}



void pre_filter_by_nearby(k_mer_pos* new_n_list, k_mer_pos* old_n_list, uint64_t n_length, uint64_t n_end_pos, UC_Read* g_read, 
All_reads* R_INF, Correct_dumy* dumy, uint64_t* new_n_length)
{
    (*new_n_length) = 0;
    ///这种就是0，new_n_list也不需要有数据
    if (n_length == 0)
    {
        return;
    }
    
    char* x_string = NULL;
    char* y_string = NULL;
    

    long long  x_offset = (long long)(n_end_pos) - WINDOW + 1;
    if (x_offset < 0)
    {
        x_offset = 0;
    }

    ///x_length是x上待验证区间的实际长度
    ///x_offset是x上待验证区间的起始位置
    ///如果是向前取待验证区间，那么x_length至少大于等于40 (compressed k-mer长度，不是实际长度)
    long long x_length = n_end_pos - x_offset + 1;
    ///这种也不要过滤了，直接把old_n_list全部赋值过来就好了
    if (x_length < (WINDOW/2))
    {
        (*new_n_length) = n_length;
        memcpy(new_n_list, old_n_list, sizeof(k_mer_pos)*n_length);
        return;
    }
    long long Window_Len = x_length + (THRESHOLD << 1);
    x_string = g_read->seq + x_offset;


    long long y_offset;
    long long y_length;

    long long i = 0;

    long long y_read_length;
    int end_site;
    unsigned int error;

    int groupLen = 0;
    int return_sites[GROUP_SIZE];
    unsigned int return_sites_error[GROUP_SIZE];
    uint64_t readID[GROUP_SIZE];
    uint64_t offset[GROUP_SIZE];

    for (i = 0; i < n_length; i++)
    {
        ////old_n_list[i].offset是y上k-mer的结束位置
        ///n_end_pos是x上k-mer的结束位置
        ///x_length是x上区间长度
        y_offset = (long long)(old_n_list[i].offset) - x_length;
        ///这种情况下弃疗
        if (y_offset < 0)
        {
            new_n_list[(*new_n_length)].readID = old_n_list[i].readID;
            new_n_list[(*new_n_length)].offset = old_n_list[i].offset;
            (*new_n_length)++;
            continue;
        }

        y_offset = y_offset - THRESHOLD;
        ///还能抢救
        if (y_offset < 0)
        {
            y_offset = 0;
        }

        ///y的read的总长度
        y_read_length = Get_READ_LENGTH((*R_INF), old_n_list[i].readID);
        y_length = MIN(Window_Len, y_read_length - y_offset);

        ///如果y的长度比x长度还小，那就直接弃疗了
        if (y_length < x_length)
        {
            new_n_list[(*new_n_length)].readID = old_n_list[i].readID;
            new_n_list[(*new_n_length)].offset = old_n_list[i].offset;
            (*new_n_length)++;
            continue;
        }

        if(y_length == Window_Len)
        {
             ///y的方向都是0，因为索引里都是0
            recover_UC_Read_sub_region(dumy->overlap_region_group[groupLen], y_offset, y_length, 0, 
                            R_INF, old_n_list[i].readID);
            readID[groupLen] = old_n_list[i].readID;
            offset[groupLen] = old_n_list[i].offset;


            groupLen++;
            if (groupLen == GROUP_SIZE)
            {
                Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1], 
                dumy->overlap_region_group[2], dumy->overlap_region_group[3], y_length, x_string, x_length,
                    return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
                groupLen = 0;

                if (return_sites_error[0]!=(unsigned int)-1)
                {
                    new_n_list[(*new_n_length)].readID = readID[0];
                    new_n_list[(*new_n_length)].offset = offset[0];
                    (*new_n_length)++;
                }

                if (return_sites_error[1]!=(unsigned int)-1)
                {
                    new_n_list[(*new_n_length)].readID = readID[1];
                    new_n_list[(*new_n_length)].offset = offset[1];
                    (*new_n_length)++;
                }

                if (return_sites_error[2]!=(unsigned int)-1)
                {
                    new_n_list[(*new_n_length)].readID = readID[2];
                    new_n_list[(*new_n_length)].offset = offset[2];
                    (*new_n_length)++;
                }

                if (return_sites_error[3]!=(unsigned int)-1)
                {
                    new_n_list[(*new_n_length)].readID = readID[3];
                    new_n_list[(*new_n_length)].offset = offset[3];
                    (*new_n_length)++;
                }
                
            }

        }
        else
        {
            ///y的方向都是0，因为索引里都是0
            recover_UC_Read_sub_region(dumy->overlap_region, y_offset, y_length, 0, R_INF, old_n_list[i].readID);
            y_string = dumy->overlap_region;

            memset (y_string + y_length, 0, Window_Len - y_length);
            end_site = Reserve_Banded_BPM(y_string, y_length, x_string, x_length, THRESHOLD, &error);

            if (error!=(unsigned int)-1)
            {
                new_n_list[(*new_n_length)].readID = old_n_list[i].readID;
                new_n_list[(*new_n_length)].offset = old_n_list[i].offset;
                (*new_n_length)++;
            }
        }
        
        
  
    }



    if (groupLen == 1)
    {
         end_site = Reserve_Banded_BPM(dumy->overlap_region_group[0], Window_Len, x_string, x_length, THRESHOLD, &error);

        if (error!=(unsigned int)-1)
        {
            new_n_list[(*new_n_length)].readID = readID[0];
            new_n_list[(*new_n_length)].offset = offset[0];
            (*new_n_length)++;
        }

    }
    else
    {
        Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1], 
                dumy->overlap_region_group[2], dumy->overlap_region_group[3], Window_Len, x_string, x_length,
                    return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
        

        for (i = 0; i < groupLen; i++)
        {
            if (return_sites_error[i]!=(unsigned int)-1)
            {
                new_n_list[(*new_n_length)].readID = readID[i];
                new_n_list[(*new_n_length)].offset = offset[i];
                (*new_n_length)++;
            }
        }

        groupLen = 0;
        

    }

    ///要排序....
    if ((*new_n_length)>1)
    {
        qsort(new_n_list, (*new_n_length), sizeof(k_mer_pos), cmp_k_mer_pos);
    }
}



/**********************for prefilter************************ */

void destory_k_mer_pos_list_alloc_prefilter(k_mer_pos_list_alloc* list)
{
    long long i = 0;
    for (i = 0; i < list->size; i++)
    {
        if (list->list[i].size != 0)
        {
            free(list->list[i].list);
        }
    }

    free(list->list);
}


void append_k_mer_pos_list_alloc_prefilter(k_mer_pos_list_alloc* list, k_mer_pos* n_list, uint64_t n_length, 
uint64_t n_end_pos, uint8_t n_direction, UC_Read* g_read, All_reads* R_INF, Correct_dumy* dumy)
{
   
    if (list->length + 1 > list->size)
    {
        list->size = list->size * 2;
        list->list = (k_mer_pos_list*)realloc(list->list, sizeof(k_mer_pos_list)*list->size);
        ///新分配空间要初始化
        memset(list->list + (list->size/2), 0, sizeof(k_mer_pos_list)*(list->size/2));
    }

    if (list->list[list->length].size < n_length)
    {
        list->list[list->length].size = n_length;
        list->list[list->length].list = (k_mer_pos*)realloc(list->list[list->length].list, 
                    sizeof(k_mer_pos)*list->list[list->length].size);
    }
    
    
    ///list->list[list->length].list = n_list;
    ///memcpy(list->list[list->length].list, n_list, sizeof(k_mer_pos)*n_length);
    pre_filter_by_nearby(list->list[list->length].list, n_list, n_length, n_end_pos, 
            g_read, R_INF, dumy, &n_length);
    
            
    if(n_length > 0)
    {
        list->list[list->length].length = n_length;
        list->list[list->length].direction = n_direction;
        list->list[list->length].end_pos = n_end_pos;

        list->length++;
    }
}


/**********************for prefilter************************ */