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hifiasm/Hash_Table.cpp
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#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include "Hash_Table.h"
#include "Process_Read.h"
#include "Correct.h"
#include "CommandLines.h"
#include "kmer.h"
#include <pthread.h>
#include "ksort.h"
pthread_mutex_t output_mutex;
#define overlap_region_key(a) ((a).y_id)
KRADIX_SORT_INIT(overlap_region_sort, overlap_region, overlap_region_key, member_size(overlap_region, y_id))
void overlap_region_sort_y_id(overlap_region *a, long long n)
{
radix_sort_overlap_region_sort(a, a + n);
}
void Init_Heap(HeapSq* HBT)
{
HBT->MaxSize = 1000;
HBT->heap = (ElemType*)malloc(HBT->MaxSize*sizeof(ElemType));
HBT->index_i = (uint64_t*)malloc(HBT->MaxSize*sizeof(uint64_t));
HBT->len = 0;
}
void destory_Heap(HeapSq* HBT)
{
free(HBT->heap);
free(HBT->index_i);
}
void clear_Heap(HeapSq* HBT)
{
HBT->len = 0;
}
inline int cmp_ElemType_back_back(ElemType* x, ElemType* y)
{
long long r_pos_x, r_pos_y;
if (x->node.strand < y->node.strand)
{
return 1;
}
else if (x->node.strand > y->node.strand)
{
return 2;
}
else
{
if (x->node.readID < y->node.readID)
{
return 1;
}
else if (x->node.readID > y->node.readID)
{
return 2;
}
else
{
r_pos_x = x->node.offset - x->node.self_offset;
r_pos_y = y->node.offset - y->node.self_offset;
///if (x->node.offset < y->node.offset)
if (r_pos_x < r_pos_y)
{
return 1;
}
///else if (x->node.offset > y->node.offset)
else if (r_pos_x > r_pos_y)
{
return 2;
}
else
{
if (x->node.self_offset < y->node.self_offset)
{
return 1;
}
else if (x->node.self_offset > y->node.self_offset)
{
return 2;
}
else ///如果r_pos_x和self_offset都相等，那么offset肯定也相等，也没必要再比了
{
return 0;
}
}
}
}
}
inline int cmp_ElemType_back(ElemType* x, ElemType* y)
{
long long r_pos_x, r_pos_y;
if (x->node.readID < y->node.readID)
{
return 1;
}
else if (x->node.readID > y->node.readID)
{
return 2;
}
else
{ if (x->node.strand < y->node.strand)
{
return 1;
}
else if (x->node.strand > y->node.strand)
{
return 2;
}
else
{
r_pos_x = x->node.offset - x->node.self_offset;
r_pos_y = y->node.offset - y->node.self_offset;
///if (x->node.offset < y->node.offset)
if (r_pos_x < r_pos_y)
{
return 1;
}
///else if (x->node.offset > y->node.offset)
else if (r_pos_x > r_pos_y)
{
return 2;
}
else
{
if (x->node.self_offset < y->node.self_offset)
{
return 1;
}
else if (x->node.self_offset > y->node.self_offset)
{
return 2;
}
else ///如果r_pos_x和self_offset都相等，那么offset肯定也相等，也没必要再比了
{
return 0;
}
}
}
}
}
inline int cmp_ElemType(ElemType* x, ElemType* y)
{
if (x->node.readID < y->node.readID)
{
return 1;
}
else if (x->node.readID > y->node.readID)
{
return 2;
}
else
{ if (x->node.strand < y->node.strand)
{
return 1;
}
else if (x->node.strand > y->node.strand)
{
return 2;
}
else
{
if(x->node.offset < y->node.offset)
{
return 1;
}
else if(x->node.offset > y->node.offset)
{
return 2;
}
else
{
if (x->node.self_offset < y->node.self_offset)
{
return 1;
}
else if (x->node.self_offset > y->node.self_offset)
{
return 2;
}
else ///如果r_pos_x和self_offset都相等，那么offset肯定也相等，也没必要再比了
{
return 0;
}
}
}
}
}
inline void Insert_Heap(HeapSq* HBT, ElemType* x)
{
long long i, j;
if (HBT->len == HBT->MaxSize) //若堆满，将数组空间扩展为原来的2倍
{
HBT->MaxSize = 2*HBT->MaxSize;
HBT->heap = (ElemType*)realloc(HBT->heap, HBT->MaxSize*sizeof(ElemType));
HBT->index_i = (uint64_t*)realloc(HBT->index_i,HBT->MaxSize*sizeof(uint64_t));
}
HBT->heap[HBT->len] = *x; //向堆尾添加新元素
HBT->len++; //堆长度加1
i = HBT->len - 1; //i指向待调整元素的位置，即其数组下标，初始指向新元素所在的堆尾位置
while (i != 0)
{
j = (i - 1) / 2; //j指向下标为i的元素的双亲
///if (x >= HBT->heap[j]) //若新元素大于待调整元素的双亲，则比较调整结束，退出循环
///1: x<y
if (cmp_ElemType(x, &HBT->heap[j])!=1)
break;
HBT->heap[i] = HBT->heap[j]; //将双亲元素下移到待调整元素的位置
i = j; //使待调整位置变为其双亲位置，进行下一次循环
}
HBT->heap[i] = *x;//把新元素调整到最终位置
}
inline int DeleteHeap(HeapSq* HBT, ElemType* get)
{
ElemType temp, x;
int i, j;
if (HBT->len == 0)
{
return 0;
}
temp = HBT->heap[0]; //暂存堆顶元素
HBT->len--;
if (HBT->len == 0) //若删除操作后堆为空则返回
{
*get = temp;
return 2;
}
x = HBT->heap[HBT->len]; //将待调整的原堆尾元素暂存x中，以便放入最终位置
i = 0; //用i指向待调整元素的位置，初始指向堆顶位置
j = 2 * i + 1;//用j指向i的左孩子位置，初始指向下标为1的位置
while (j <= HBT->len - 1)//寻找待调整元素的最终位置，每次使孩子元素上移一层，调整到孩子为空时止
{
///if (j < HBT->len - 1 && HBT->heap[j] > HBT->heap[j+1])//若存在右孩子且较小，使j指向右孩子
if (j < HBT->len - 1 && cmp_ElemType(&HBT->heap[j], &HBT->heap[j + 1]) == 2)
j++;
///if (x <= HBT->heap[j]) //若x比其较小的孩子还小，则调整结束，退出循环
if (cmp_ElemType(&x, &HBT->heap[j])!=2)
break;
HBT->heap[i] = HBT->heap[j];//否则，将孩子元素移到双亲位置
i = j; //将待调整位置变为其较小的孩子位置
j = 2 * i + 1;//将j变为新的待调整位置的左孩子位置，继续下一次循环
}
HBT->heap[i] = x; //把x放到最终位置
//返回原堆顶元素
*get = temp;
return 1;
}
void init_overlap_region_alloc(overlap_region_alloc* list)
{
list->size = 1000;
list->length = 0;
///list->list = (overlap_region*)malloc(sizeof(overlap_region)*list->size);
list->list = (overlap_region*)calloc(list->size, sizeof(overlap_region));
long long i;
for (i = 0; i < list->size; i++)
{
init_fake_cigar(&(list->list[i].f_cigar));
}
}
void clear_overlap_region_alloc(overlap_region_alloc* list)
{
list->length = 0;
list->mapped_overlaps_length = 0;
int i = 0;
for (i = 0; i < list->size; i++)
{
list->list[i].w_list_length = 0;
clear_fake_cigar(&(list->list[i].f_cigar));
}
}
void destory_overlap_region_alloc(overlap_region_alloc* list)
{
int i = 0;
for (i = 0; i < list->size; i++)
{
if (list->list[i].w_list_size != 0)
{
free(list->list[i].w_list);
}
destory_fake_cigar(&(list->list[i].f_cigar));
}
free(list->list);
}
int get_fake_gap_pos(Fake_Cigar* x, int index)
{
return (x->buffer[index]>>32);
}
int get_fake_gap_shift(Fake_Cigar* x, int index)
{
uint32_t tmp = ((uint32_t)(x->buffer[index]));
int result;
if(tmp & ((uint32_t)1))
{
tmp = tmp >> 1;
result = tmp;
result = result * -1;
}
else
{
tmp = tmp >> 1;
result = tmp;
}
return result;
}
///r->length = Get_READ_LENGTH((*R_INF), ID);
void append_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp, All_reads* R_INF)
{
if (list->length + 1 > list->size)
{
list->size = list->size * 2;
list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
///新分配空间要初始化
memset(list->list + (list->size/2), 0, sizeof(overlap_region)*(list->size/2));
}
if (list->length!=0 &&
list->list[list->length - 1].y_id==tmp->y_id
)
{
if(list->list[list->length - 1].shared_seed >= tmp->shared_seed)
{
return;
}
else
{
list->length--;
}
}
if(tmp->x_pos_s <= tmp->y_pos_s)
{
tmp->y_pos_s = tmp->y_pos_s - tmp->x_pos_s;
tmp->x_pos_s = 0;
}
else
{
tmp->x_pos_s = tmp->x_pos_s - tmp->y_pos_s;
tmp->y_pos_s = 0;
}
tmp->x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_s - 1;
tmp->y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_s - 1;
if(tmp->x_pos_e <= tmp->y_pos_e)
{
tmp->y_pos_e = tmp->y_pos_s + tmp->x_pos_e;
tmp->x_pos_e = tmp->x_pos_s + tmp->x_pos_e;
}
else
{
tmp->x_pos_e = tmp->x_pos_s + tmp->y_pos_e;
tmp->y_pos_e = tmp->y_pos_s + tmp->y_pos_e;
}
///y的区间方向永远是0
///x有可能是1
///如果x是1，那我们把它逆过来
if (tmp->x_pos_strand == 1)
{
list->list[list->length].x_id = tmp->x_id;
list->list[list->length].x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_s - 1;
list->list[list->length].x_pos_s = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_e - 1;
list->list[list->length].x_pos_strand = 0;
list->list[list->length].y_id = tmp->y_id;
list->list[list->length].y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_s - 1;
list->list[list->length].y_pos_s = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_e - 1;
list->list[list->length].y_pos_strand = 1;
// resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
// add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
// long long distance_gap;
// long long pre_distance_gap = 0;
// long long i = 0;
// for (i = 0; i < tmp->f_cigar.length; i++)
// {
// distance_gap = get_fake_gap_shift(&(tmp->f_cigar), i);
// if(distance_gap != pre_distance_gap)
// {
// pre_distance_gap = distance_gap;
// add_fake_cigar(&(list->list[list->length].f_cigar),
// Get_READ_LENGTH((*R_INF), tmp->x_id) - get_fake_gap_pos(&(tmp->f_cigar), i) - 1,
// pre_distance_gap);
// }
// }
// if(get_fake_gap_pos(&(list->list[list->length].f_cigar),
// list->list[list->length].f_cigar.length - 1) != list->list[list->length].x_pos_e)
// {
// add_fake_cigar(&(list->list[list->length].f_cigar),
// list->list[list->length].x_pos_e,
// get_fake_gap_shift(&(list->list[list->length].f_cigar),
// list->list[list->length].f_cigar.length - 1));
// }
}
else
{
list->list[list->length].x_id = tmp->x_id;
list->list[list->length].x_pos_e = tmp->x_pos_e;
list->list[list->length].x_pos_s = tmp->x_pos_s;
list->list[list->length].x_pos_strand = tmp->x_pos_strand;
list->list[list->length].y_id = tmp->y_id;
list->list[list->length].y_pos_e = tmp->y_pos_e;
list->list[list->length].y_pos_s = tmp->y_pos_s;
list->list[list->length].y_pos_strand = tmp->y_pos_strand;
// resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
// add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
// long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
// long long distance_pos = tmp->y_pos_e - tmp->y_pos_s;
// long long init_distance_gap = distance_pos - distance_self_pos;
// long long pre_distance_gap = init_distance_gap;
// long long distance_gap;
// long long i = 0;
// for (i = tmp->f_cigar.length - 1; i >= 0; i--)
// {
// distance_gap = get_fake_gap_shift(&(tmp->f_cigar), i);
// if(distance_gap != pre_distance_gap)
// {
// pre_distance_gap = distance_gap;
// add_fake_cigar(&(list->list[list->length].f_cigar),
// get_fake_gap_pos(&(tmp->f_cigar), i), init_distance_gap - pre_distance_gap);
// }
// }
// if(get_fake_gap_pos(&(list->list[list->length].f_cigar),
// list->list[list->length].f_cigar.length - 1) != list->list[list->length].x_pos_e)
// {
// add_fake_cigar(&(list->list[list->length].f_cigar),
// list->list[list->length].x_pos_e,
// get_fake_gap_shift(&(list->list[list->length].f_cigar),
// list->list[list->length].f_cigar.length - 1));
// }
/******************************for debug********************************/
// distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
// distance_pos = tmp->y_pos_e - tmp->y_pos_s;
// distance_gap = distance_pos - distance_self_pos;
// fprintf(stderr, "\nx_s: %d, x_e: %d, y_s: %d, y_e: %d, distance_gap: %d\n",
// list->list[list->length].x_pos_s, list->list[list->length].x_pos_e,
// list->list[list->length].y_pos_s, list->list[list->length].y_pos_e, distance_gap);
// for (i = 0; i < list->list[list->length].f_cigar.length; i++)
// {
// fprintf(stderr, "##i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
// i, get_fake_gap_pos(&(list->list[list->length].f_cigar), i),
// get_fake_gap_shift(&(list->list[list->length].f_cigar), i));
// }
// for (i = 0; i < tmp->f_cigar.length; i++)
// {
// fprintf(stderr, "**i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
// i, get_fake_gap_pos(&(tmp->f_cigar), i),
// get_fake_gap_shift(&(tmp->f_cigar), i));
// }
/******************************for debug********************************/
}
list->list[list->length].shared_seed = tmp->shared_seed;
list->list[list->length].align_length = 0;
list->list[list->length].is_match = 0;
list->list[list->length].non_homopolymer_errors = 0;
list->length++;
}
void append_overlap_region_alloc_from_existing(overlap_region_alloc* list, overlap_region* tmp, All_reads* R_INF)
{
if (list->length + 1 > list->size)
{
list->size = list->size * 2;
list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
///新分配空间要初始化
memset(list->list + (list->size/2), 0, sizeof(overlap_region)*(list->size/2));
}
if (list->length!=0 &&
list->list[list->length - 1].y_id==tmp->y_id
)
{
if(list->list[list->length - 1].shared_seed >= tmp->shared_seed)
{
return;
}
else
{
list->length--;
}
}
if(tmp->x_pos_s <= tmp->y_pos_s)
{
tmp->y_pos_s = tmp->y_pos_s - tmp->x_pos_s;
tmp->x_pos_s = 0;
}
else
{
tmp->x_pos_s = tmp->x_pos_s - tmp->y_pos_s;
tmp->y_pos_s = 0;
}
tmp->x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_s - 1;
tmp->y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_s - 1;
if(tmp->x_pos_e <= tmp->y_pos_e)
{
tmp->y_pos_e = tmp->y_pos_s + tmp->x_pos_e;
tmp->x_pos_e = tmp->x_pos_s + tmp->x_pos_e;
}
else
{
tmp->x_pos_e = tmp->x_pos_s + tmp->y_pos_e;
tmp->y_pos_e = tmp->y_pos_s + tmp->y_pos_e;
}
// if(tmp->x_pos_strand != 0)
// {
// fprintf(stderr, "error\n");
// }
list->list[list->length].x_id = tmp->x_id;
list->list[list->length].x_pos_e = tmp->x_pos_e;
list->list[list->length].x_pos_s = tmp->x_pos_s;
list->list[list->length].x_pos_strand = tmp->x_pos_strand;
list->list[list->length].y_id = tmp->y_id;
list->list[list->length].y_pos_e = tmp->y_pos_e;
list->list[list->length].y_pos_s = tmp->y_pos_s;
list->list[list->length].y_pos_strand = tmp->y_pos_strand;
list->list[list->length].shared_seed = tmp->shared_seed;
list->list[list->length].align_length = 0;
list->list[list->length].is_match = 0;
list->list[list->length].non_homopolymer_errors = 0;
list->length++;
// fprintf(stderr, "shared_seed: %d, x_pos_s: %d, x_pos_e: %d, y_pos_s: %d, y_pos_e: %d, list->length: %d\n",
// tmp->shared_seed, tmp->x_pos_s, tmp->x_pos_e, tmp->y_pos_s, tmp->y_pos_e, list->length);
// fprintf(stderr, "*****x_pos_s: %d, x_pos_e: %d, y_pos_s: %d, y_pos_e: %d, list->length: %d\n",
// list->list[list->length - 1].x_pos_s, list->list[list->length - 1].x_pos_e,
// list->list[list->length - 1].y_pos_s, list->list[list->length - 1].y_pos_e,
// list->length);
}
int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp, All_reads* R_INF)
{
if (list->length + 1 > list->size)
{
list->size = list->size * 2;
list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
///新分配空间要初始化
memset(list->list + (list->size/2), 0, sizeof(overlap_region)*(list->size/2));
}
if (list->length!=0 && list->list[list->length - 1].y_id==tmp->y_id)
{
///if(list->list[list->length - 1].shared_seed >= tmp->shared_seed)
if((list->list[list->length - 1].shared_seed > tmp->shared_seed)
||
((list->list[list->length - 1].shared_seed == tmp->shared_seed) &&
(list->list[list->length - 1].overlapLen <= tmp->overlapLen)))
{
return 0;
}
else
{
list->length--;
}
}
if(tmp->x_pos_s <= tmp->y_pos_s)
{
tmp->y_pos_s = tmp->y_pos_s - tmp->x_pos_s;
tmp->x_pos_s = 0;
}
else
{
tmp->x_pos_s = tmp->x_pos_s - tmp->y_pos_s;
tmp->y_pos_s = 0;
}
long long x_right_length = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_e - 1;
long long y_right_length = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_e - 1;
if(x_right_length <= y_right_length)
{
tmp->x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - 1;
tmp->y_pos_e = tmp->y_pos_e + x_right_length;
}
else
{
tmp->x_pos_e = tmp->x_pos_e + y_right_length;
tmp->y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - 1;
}
if (tmp->x_pos_strand == 1)
{
list->list[list->length].x_id = tmp->x_id;
list->list[list->length].x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_s - 1;
list->list[list->length].x_pos_s = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_e - 1;
list->list[list->length].x_pos_strand = 0;
list->list[list->length].y_id = tmp->y_id;
list->list[list->length].y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_s - 1;
list->list[list->length].y_pos_s = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_e - 1;
list->list[list->length].y_pos_strand = 1;
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
long long distance_gap;
long long pre_distance_gap = 0;
long long i = 0;
for (i = 0; i < tmp->f_cigar.length; i++)
{
distance_gap = get_fake_gap_shift(&(tmp->f_cigar), i);
if(distance_gap != pre_distance_gap)
{
pre_distance_gap = distance_gap;
add_fake_cigar(&(list->list[list->length].f_cigar),
Get_READ_LENGTH((*R_INF), tmp->x_id) - get_fake_gap_pos(&(tmp->f_cigar), i) - 1,
pre_distance_gap);
}
}
if(get_fake_gap_pos(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1) != list->list[list->length].x_pos_e)
{
add_fake_cigar(&(list->list[list->length].f_cigar),
list->list[list->length].x_pos_e,
get_fake_gap_shift(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1));
}
/******************************for debug********************************/
// long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
// long long distance_pos = tmp->y_pos_e - tmp->y_pos_s;
// distance_gap = distance_pos - distance_self_pos;
// if(distance_gap !=
// get_fake_gap_shift(&(list->list[list->length].f_cigar),
// list->list[list->length].f_cigar.length - 1))
// {
// fprintf(stderr, "error\n");
// }
// long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
// long long distance_pos = tmp->y_pos_e - tmp->y_pos_s;
// distance_gap = distance_pos - distance_self_pos;
// fprintf(stderr, "\nx_s: %d, x_e: %d, y_s: %d, y_e: %d, distance_gap: %d, xLen: %d\n",
// list->list[list->length].x_pos_s, list->list[list->length].x_pos_e,
// list->list[list->length].y_pos_s, list->list[list->length].y_pos_e, distance_gap,
// Get_READ_LENGTH((*R_INF), tmp->x_id));
// for (i = 0; i < list->list[list->length].f_cigar.length; i++)
// {
// fprintf(stderr, "##i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
// i, get_fake_gap_pos(&(list->list[list->length].f_cigar), i),
// get_fake_gap_shift(&(list->list[list->length].f_cigar), i));
// }
// for (i = 0; i < tmp->f_cigar.length; i++)
// {
// fprintf(stderr, "**i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
// i, get_fake_gap_pos(&(tmp->f_cigar), i),
// get_fake_gap_shift(&(tmp->f_cigar), i));
// }
/******************************for debug********************************/
}
else
{
list->list[list->length].x_id = tmp->x_id;
list->list[list->length].x_pos_e = tmp->x_pos_e;
list->list[list->length].x_pos_s = tmp->x_pos_s;
list->list[list->length].x_pos_strand = tmp->x_pos_strand;
list->list[list->length].y_id = tmp->y_id;
list->list[list->length].y_pos_e = tmp->y_pos_e;
list->list[list->length].y_pos_s = tmp->y_pos_s;
list->list[list->length].y_pos_strand = tmp->y_pos_strand;
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
long long distance_pos = tmp->y_pos_e - tmp->y_pos_s;
long long init_distance_gap = distance_pos - distance_self_pos;
long long pre_distance_gap = init_distance_gap;
long long distance_gap;
long long i = 0;
for (i = tmp->f_cigar.length - 1; i >= 0; i--)
{
distance_gap = get_fake_gap_shift(&(tmp->f_cigar), i);
if(distance_gap != pre_distance_gap)
{
pre_distance_gap = distance_gap;
add_fake_cigar(&(list->list[list->length].f_cigar),
get_fake_gap_pos(&(tmp->f_cigar), i), init_distance_gap - pre_distance_gap);
}
}
if(get_fake_gap_pos(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1) != list->list[list->length].x_pos_e)
{
add_fake_cigar(&(list->list[list->length].f_cigar),
list->list[list->length].x_pos_e,
get_fake_gap_shift(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1));
}
/******************************for debug********************************/
// distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
// distance_pos = tmp->y_pos_e - tmp->y_pos_s;
// distance_gap = distance_pos - distance_self_pos;
// if(distance_gap !=
// get_fake_gap_shift(&(list->list[list->length].f_cigar),
// list->list[list->length].f_cigar.length - 1))
// {
// fprintf(stderr, "error\n");
// }
// distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
// distance_pos = tmp->y_pos_e - tmp->y_pos_s;
// distance_gap = distance_pos - distance_self_pos;
// fprintf(stderr, "\nx_s: %d, x_e: %d, y_s: %d, y_e: %d, distance_gap: %d\n",
// list->list[list->length].x_pos_s, list->list[list->length].x_pos_e,
// list->list[list->length].y_pos_s, list->list[list->length].y_pos_e, distance_gap);
// for (i = 0; i < list->list[list->length].f_cigar.length; i++)
// {
// fprintf(stderr, "##i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
// i, get_fake_gap_pos(&(list->list[list->length].f_cigar), i),
// get_fake_gap_shift(&(list->list[list->length].f_cigar), i));
// }
// for (i = 0; i < tmp->f_cigar.length; i++)
// {
// fprintf(stderr, "**i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
// i, get_fake_gap_pos(&(tmp->f_cigar), i),
// get_fake_gap_shift(&(tmp->f_cigar), i));
// }
/******************************for debug********************************/
}
list->list[list->length].shared_seed = tmp->shared_seed;
list->list[list->length].align_length = 0;
list->list[list->length].is_match = 0;
list->list[list->length].non_homopolymer_errors = 0;
list->list[list->length].strong = 0;
list->length++;
return 1;
}
void append_overlap_region_alloc_debug(overlap_region_alloc* list, overlap_region* tmp)
{
if (list->length + 1 > list->size)
{
list->size = list->size * 2;
list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
}
list->list[list->length].x_id = tmp->x_id;
list->list[list->length].x_pos_e = tmp->x_pos_e;
list->list[list->length].x_pos_s = tmp->x_pos_s;
list->list[list->length].x_pos_strand = tmp->x_pos_strand;
list->list[list->length].y_id = tmp->y_id;
list->list[list->length].y_pos_e = tmp->y_pos_e;
list->list[list->length].y_pos_s = tmp->y_pos_s;
list->list[list->length].y_pos_strand = tmp->y_pos_strand;
list->list[list->length].shared_seed = tmp->shared_seed;
list->length++;
}
void debug_overlap_region(Candidates_list* candidates, overlap_region_alloc* overlap_list, uint64_t readID)
{
uint64_t i = 0;
uint64_t total_length = 0;
uint64_t pre_total_length = 0;
uint64_t current_ID;
uint64_t current_stand;
long long current_pos_diff;
long long current_self_pos;
long long tmp_pos_distance;
long long tmp_self_pos_distance;
long long constant_distance = 5;
double error_rate = 0.05;
for ( i = 0; i < overlap_list->length; i++)
{
pre_total_length = total_length;
total_length = total_length + overlap_list->list[i].shared_seed;
uint64_t j = 0;
current_ID = candidates->list[pre_total_length].readID;
current_stand = candidates->list[pre_total_length].strand;
current_pos_diff = candidates->list[pre_total_length].offset - candidates->list[pre_total_length].self_offset;
current_self_pos = candidates->list[pre_total_length].self_offset;
for (j = pre_total_length; j < total_length; j++)
{
if(current_ID != candidates->list[j].readID ||
current_stand != candidates->list[j].strand)
{
fprintf(stderr, "ERROR Overlap 1!\n");
}
///这个一定是正值
tmp_pos_distance = candidates->list[j].offset - candidates->list[j].self_offset - current_pos_diff;
///这个不一定是正值
tmp_self_pos_distance = candidates->list[j].self_offset - current_self_pos;
if (tmp_self_pos_distance < 0)
{
fprintf(stderr, "ERROR Overlap 3!\n");
}
if (tmp_self_pos_distance >= 0)
{
tmp_self_pos_distance = tmp_self_pos_distance * error_rate + constant_distance;
if (tmp_pos_distance >= tmp_self_pos_distance)
{
fprintf(stderr, "ERROR Overlap 4!\n");
}
}
}
if (total_length < candidates->length)
{
j = total_length;
if (current_ID == candidates->list[j].readID &&
current_stand == candidates->list[j].strand)
{
///这个一定是正值
tmp_pos_distance = candidates->list[j].offset - candidates->list[j].self_offset - current_pos_diff;
///这个不一定是正值
tmp_self_pos_distance = candidates->list[j].self_offset - current_self_pos;
if (tmp_self_pos_distance >= 0)
{
tmp_self_pos_distance = tmp_self_pos_distance * error_rate + constant_distance;
if (tmp_pos_distance < tmp_self_pos_distance)
{
fprintf(stderr, "ERROR Overlap 5!\n");
}
}
}
}
}
if (total_length != candidates->length)
{
fprintf(stderr, "ERROR Overlap 2!\n");
fprintf(stderr, "total_length: %llu\n", total_length);
fprintf(stderr, "candidates->length: %llu\n", candidates->length);
}
}
void print_overlap_region(Candidates_list* candidates, overlap_region_alloc* overlap_list, All_reads* R_INF)
{
pthread_mutex_lock(&output_mutex);
uint64_t i = 0;
for ( i = 0; i < overlap_list->length; i++)
{
fprintf(stderr, "************i: %llu***********\n", i);
fprintf(stderr, "x: %llu, %llu, %llu, %llu, %llu\n",
overlap_list->list[i].x_id,overlap_list->list[i].x_pos_s,
overlap_list->list[i].x_pos_e, overlap_list->list[i].x_pos_strand,
Get_READ_LENGTH((*R_INF), overlap_list->list[i].x_id)
);
fprintf(stderr, "y: %llu, %llu, %llu, %llu, %llu\n",
overlap_list->list[i].y_id,overlap_list->list[i].y_pos_s,
overlap_list->list[i].y_pos_e, overlap_list->list[i].y_pos_strand,
Get_READ_LENGTH((*R_INF), overlap_list->list[i].y_id)
);
}
fprintf(stderr, "#######################\nLength: %llu\n", candidates->length);
for (i = 0; i < candidates->length; i++)
{
fprintf(stderr, "\ni: %llu\n", i);
fprintf(stderr, "strand: %llu\n", candidates->list[i].strand);
fprintf(stderr, "readID: %llu\n", candidates->list[i].readID);
fprintf(stderr, "diff: %lld\n", candidates->list[i].offset - candidates->list[i].self_offset);
fprintf(stderr, "offset: %lld\n", candidates->list[i].offset);
fprintf(stderr, "self_offset: %lld\n", candidates->list[i].self_offset);
}
pthread_mutex_unlock(&output_mutex);
}
int cmp_by_x_pos_s(const void * a, const void * b)
{
if ((*(overlap_region*)a).x_pos_s > (*(overlap_region*)b).x_pos_s)
{
return 1;
}
else if ((*(overlap_region*)a).x_pos_s < (*(overlap_region*)b).x_pos_s)
{
return -1;
}
else
{
if ((*(overlap_region*)a).x_pos_e > (*(overlap_region*)b).x_pos_e)
{
return 1;
}
else if ((*(overlap_region*)a).x_pos_e < (*(overlap_region*)b).x_pos_e)
{
return -1;
}
else
{
return 0;
}
}
}
int cmp_by_x_pos_e(const void * a, const void * b)
{
if ((*(overlap_region*)a).x_pos_e > (*(overlap_region*)b).x_pos_e)
{
return 1;
}
else if ((*(overlap_region*)a).x_pos_e < (*(overlap_region*)b).x_pos_e)
{
return -1;
}
else
{
if ((*(overlap_region*)a).x_pos_s > (*(overlap_region*)b).x_pos_s)
{
return 1;
}
else if ((*(overlap_region*)a).x_pos_s < (*(overlap_region*)b).x_pos_s)
{
return -1;
}
else
{
return 0;
}
}
}
///r->length = Get_READ_LENGTH((*R_INF), ID);
void calculate_overlap_region(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF)
{
overlap_region tmp_region;
uint64_t i = 0;
long long current_pos_diff;
long long current_self_pos;
uint64_t current_ID;
uint64_t current_stand;
long long tmp_pos_distance;
long long tmp_self_pos_distance;
long long constant_distance = 5;
double error_rate = 0.05;
if (candidates->length == 0)
{
return;
}
i = 0;
while (i < candidates->length)
{
current_pos_diff = candidates->list[i].offset - candidates->list[i].self_offset;
current_self_pos = candidates->list[i].self_offset;
current_ID = candidates->list[i].readID;
current_stand = candidates->list[i].strand;
tmp_region.shared_seed = 1;
///这个是查询read的信息
tmp_region.x_id = readID;
tmp_region.x_pos_s = candidates->list[i].self_offset;
tmp_region.x_pos_e = candidates->list[i].self_offset;
tmp_region.x_pos_strand = current_stand;
///这个是被查询的read的信息
tmp_region.y_id = current_ID;
tmp_region.y_pos_s = candidates->list[i].offset;
tmp_region.y_pos_e = candidates->list[i].offset;
tmp_region.y_pos_strand = 0; ///永远是0
i++;
while (i < candidates->length)
{
if (current_ID == candidates->list[i].readID &&
current_stand == candidates->list[i].strand)
{
///这个一定是正值
tmp_pos_distance = candidates->list[i].offset - candidates->list[i].self_offset - current_pos_diff;
///这个不一定是正值
tmp_self_pos_distance = candidates->list[i].self_offset - current_self_pos;
if(tmp_self_pos_distance < 0)
{
///fprintf(stderr, "tmp_self_pos_distance: %d\n", tmp_self_pos_distance);
tmp_self_pos_distance = tmp_self_pos_distance * -1;
///fprintf(stderr, "tmp_self_pos_distance: %d\n", tmp_self_pos_distance);
}
///if (tmp_self_pos_distance >= 0)
{
tmp_self_pos_distance = tmp_self_pos_distance * error_rate + constant_distance;
if (tmp_pos_distance < tmp_self_pos_distance)
{
/****************************may have bugs********************************/
///i++;
// tmp_region.x_pos_e = candidates->list[i].self_offset;
// tmp_region.y_pos_e = candidates->list[i].offset;
/****************************may have bugs********************************/
tmp_region.shared_seed++;
if(candidates->list[i].self_offset < tmp_region.x_pos_s)
{
tmp_region.x_pos_s = candidates->list[i].self_offset;
}
if(candidates->list[i].self_offset > tmp_region.x_pos_e)
{
tmp_region.x_pos_e = candidates->list[i].self_offset;
}
if(candidates->list[i].offset < tmp_region.y_pos_s)
{
tmp_region.y_pos_s = candidates->list[i].offset;
}
if(candidates->list[i].offset > tmp_region.y_pos_e)
{
tmp_region.y_pos_e = candidates->list[i].offset;
}
/****************************may have bugs********************************/
i++;
/****************************may have bugs********************************/
continue;
}
}
}
break;
}
///自己和自己重叠的要排除
///if (tmp_region.x_id != tmp_region.y_id && tmp_region.shared_seed > 1)
if (tmp_region.x_id != tmp_region.y_id)
{
append_overlap_region_alloc(overlap_list, &tmp_region, R_INF);
}
}
///以x_pos_e，即结束位置为主元排序
///qsort(overlap_list->list, overlap_list->length, sizeof(overlap_region), cmp_by_x_pos_e);
qsort(overlap_list->list, overlap_list->length, sizeof(overlap_region), cmp_by_x_pos_s);
///debug_overlap_region(candidates, overlap_list, readID);
///print_overlap_region(candidates, overlap_list, R_INF);
}
void debug_chain(k_mer_hit* a, long long a_n, Chain_Data* dp)
{
long long i, j, current_j;
long long selfLen, indels;
long long distance_self_pos, distance_pos, distance_gap;
for (i = 0; i < a_n; ++i)
{
selfLen = indels = 0;
j = i;
while (j >= 0)
{
current_j = j;
j = dp->pre[j];
if(j != -1)
{
distance_self_pos = a[current_j].self_offset - a[j].self_offset;
distance_pos = a[current_j].offset - a[j].offset;
distance_gap = distance_pos > distance_self_pos? distance_pos - distance_self_pos : distance_self_pos - distance_pos;
indels += distance_gap;
selfLen += distance_self_pos;
}
}
if(indels != dp->indels[i])
{
fprintf(stderr, "indels: %d, dp->indels[i]: %d\n",
indels, dp->indels[i]);
}
if(selfLen != dp->self_length[i])
{
fprintf(stderr, "selfLen: %d, dp->self_length[i]: %d\n",
selfLen, dp->self_length[i]);
}
}
}
long long get_chainLen(long long x_beg, long long x_end, long long xLen,
long long y_beg, long long y_end, long long yLen)
{
if(x_beg <= y_beg)
{
y_beg = y_beg - x_beg;
x_beg = 0;
}
else
{
x_beg = x_beg - y_beg;
y_beg = 0;
}
long long x_right_length = xLen - x_end - 1;
long long y_right_length = yLen - y_end - 1;
if(x_right_length <= y_right_length)
{
x_end = xLen - 1;
y_end = y_end + x_right_length;
}
else
{
x_end = x_end + y_right_length;
y_end = yLen - 1;
}
return x_end - x_beg + 1;
}
///double band_width_threshold = 0.05;
void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result,
double band_width_threshold, int max_skip, int x_readLen, int y_readLen)
{
long long i, j;
long long self_pos, pos, max_j, max_i, max_score, score, n_skip;
long long distance_pos, distance_self_pos, distance_gap, log_distance_gap, distance_min;
///double band_width_threshold = 0.05;
double band_width_penalty = 1 / band_width_threshold;
long long min_score = k_mer_length;
long long max_indels, max_self_length;
double gap_rate;
long long total_indels, total_self_length;
resize_Chain_Data(dp, a_n);
// fill the score and backtrack arrays
for (i = 0; i < a_n; ++i)
{
pos = a[i].offset;
self_pos = a[i].self_offset;
max_j = -1;
max_score = min_score;
n_skip = 0;
max_indels = 0;
max_self_length = 0;
///may have a pre-cut condition for j
for (j = i - 1; j >= 0; --j)
{
distance_pos = pos - a[j].offset;
distance_self_pos = self_pos - a[j].self_offset;
///a has been sorted by a[].offset
///note for a, we do not have any two elements that have both equal offsets and self_offsets
///but there maybe two elements that have equal offsets or equal self_offsets
if(distance_pos == 0 || distance_self_pos <= 0)
{
continue;
}
distance_gap = distance_pos > distance_self_pos? distance_pos - distance_self_pos : distance_self_pos - distance_pos;
total_indels = dp->indels[j] + distance_gap;
total_self_length = dp->self_length[j] + distance_self_pos;
if(total_indels > band_width_threshold * total_self_length)
{
continue;
}
///min distance
distance_min = distance_pos < distance_self_pos? distance_pos:distance_self_pos;
score = distance_min < min_score? distance_min : min_score;
gap_rate = (double)((double)(total_indels)/(double)(total_self_length));
///if the gap rate > 0.06, score will be negative
score -= (long long)(gap_rate * score * band_width_penalty);
score += dp->score[j];
///find a new max score
if(score > max_score)
{
max_score = score;
max_j = j;
max_indels = total_indels;
max_self_length = total_self_length;
/****************************may have bugs********************************/
n_skip = 0;
/****************************may have bugs********************************/
}/****************************may have bugs********************************/
else
{
n_skip++;
if(n_skip > max_skip)
{
break;
}
}
/****************************may have bugs********************************/
}
dp->score[i] = max_score;
dp->pre[i] = max_j;
dp->indels[i] = max_indels;
dp->self_length[i] = max_self_length;
}
///debug_chain(a, a_n, dp);
max_score = -1;
max_i = -1;
long long mini_xLen = x_readLen * 2 + 2, tmp_xLen;
for (i = 0; i < a_n; ++i)
{
if(dp->score[i] > max_score)
{
max_score = dp->score[i];
max_i = i;
mini_xLen = get_chainLen(a[i].self_offset, a[i].self_offset, x_readLen,
a[i].offset, a[i].offset, y_readLen);
}
else if(dp->score[i] == max_score)
{
tmp_xLen = get_chainLen(a[i].self_offset, a[i].self_offset, x_readLen,
a[i].offset, a[i].offset, y_readLen);
if(tmp_xLen < mini_xLen)
{
max_score = dp->score[i];
max_i = i;
mini_xLen = tmp_xLen;
}
}
}
clear_fake_cigar(&(result->f_cigar));
i = max_i;
result->x_pos_e = a[i].self_offset;
result->y_pos_e = a[i].offset;
result->shared_seed = max_score;
result->overlapLen = mini_xLen;
distance_self_pos = result->x_pos_e - a[i].self_offset;
distance_pos = result->y_pos_e - a[i].offset;
long long pre_distance_gap = distance_pos - distance_self_pos;
///record first site
///the length of f_cigar should be at least 1
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
long long chainLen = 0;
if(result->x_pos_strand == 1)
{
while (i >= 0)
{
distance_self_pos = result->x_pos_e - a[i].self_offset;
distance_pos = result->y_pos_e - a[i].offset;
distance_gap = distance_pos - distance_self_pos;
if(distance_gap != pre_distance_gap)
{
pre_distance_gap = distance_gap;
///record this site
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
}
chainLen++;
result->x_pos_s = a[i].self_offset;
result->y_pos_s = a[i].offset;
i = dp->pre[i];
}
}
else
{
while (i >= 0)
{
distance_self_pos = result->x_pos_e - a[i].self_offset;
distance_pos = result->y_pos_e - a[i].offset;
distance_gap = distance_pos - distance_self_pos;
if(distance_gap == pre_distance_gap)
{
result->f_cigar.length--;
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
}
else
{
pre_distance_gap = distance_gap;
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
}
chainLen++;
result->x_pos_s = a[i].self_offset;
result->y_pos_s = a[i].offset;
i = dp->pre[i];
}
}
}
void debug_seed_offset(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result,
All_reads* R_INF)
{
long long i;
long long max_score = -1;
long long max_i = -1;
for (i = 0; i < a_n; i++)
{
if(max_score < dp->score[i])
{
max_score = dp->score[i];
max_i = i;
}
}
if(max_score != result->shared_seed)
{
fprintf(stderr, "max_score: %d, result->shared_seed: %d, a_n: %d, dp->length: %d\n",
max_score, result->shared_seed, a_n, dp->length);
}
long long chainLen = 0;
i = max_i;
while (i >= 0)
{
chainLen++;
i = dp->pre[i];
}
long long* chain_x_pos = (long long*)malloc(sizeof(long long)*chainLen);
long long* chain_y_pos = (long long*)malloc(sizeof(long long)*chainLen);
long long chain_i;
i = max_i;
if(result->y_pos_strand == 0)
{
chain_i = chainLen - 1;
while (i >= 0)
{
chain_x_pos[chain_i] = a[i].self_offset;
chain_y_pos[chain_i] = a[i].offset;
chain_i--;
i = dp->pre[i];
}
}
else
{
chain_i = 0;
while (i >= 0)
{
chain_x_pos[chain_i] =
Get_READ_LENGTH((*R_INF), result->x_id) - a[i].self_offset - 1;
chain_y_pos[chain_i] =
Get_READ_LENGTH((*R_INF), result->y_id) - a[i].offset - 1;
chain_i++;
i = dp->pre[i];
}
}
chain_i = 0;
long long distance_self_pos;
long long distance_pos;
long long distance_gap;
for (i = 0; i < chainLen; i++)
{
distance_self_pos = chain_x_pos[i] - result->x_pos_s;
distance_pos = chain_y_pos[i] - result->y_pos_s;
distance_gap = distance_pos - distance_self_pos;
if(distance_gap != y_start_offset(chain_x_pos[i], &(result->f_cigar)))
{
fprintf(stderr, "distance_gap: %d, y_offset: %d\n", distance_gap,
y_start_offset(chain_x_pos[i], &(result->f_cigar)));
}
}
free(chain_x_pos);
free(chain_y_pos);
}
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold)
{
overlap_region tmp_region;
uint64_t i = 0;
long long current_pos_diff;
long long current_self_pos;
uint64_t current_ID;
uint64_t current_stand;
long long tmp_pos_distance;
long long tmp_self_pos_distance;
long long constant_distance = 5;
if (candidates->length == 0)
{
return;
}
long long sub_region_beg;
long long sub_region_end;
init_fake_cigar(&(tmp_region.f_cigar));
i = 0;
while (i < candidates->length)
{
current_ID = candidates->list[i].readID;
current_stand = candidates->list[i].strand;
///这个是查询read的信息
tmp_region.x_id = readID;
tmp_region.x_pos_strand = current_stand;
///这个是被查询的read的信息
tmp_region.y_id = current_ID;
tmp_region.y_pos_strand = 0; ///永远是0
sub_region_beg = i;
sub_region_end = i;
i++;
while (i < candidates->length
&&
current_ID == candidates->list[i].readID
&&
current_stand == candidates->list[i].strand)
{
sub_region_end = i;
i++;
}
if (tmp_region.x_id == tmp_region.y_id)
{
continue;
}
// if(
// ((memcmp("m64016_190918_162737/130811282/ccs",
// Get_NAME((*R_INF), tmp_region.x_id), Get_NAME_LENGTH((*R_INF), tmp_region.x_id)) == 0)
// &&
// (memcmp("m64016_190918_162737/179635219/ccs",
// Get_NAME((*R_INF), tmp_region.y_id), Get_NAME_LENGTH((*R_INF), tmp_region.y_id)) == 0))
// ||
// ((memcmp("m64016_190918_162737/179635219/ccs",
// Get_NAME((*R_INF), tmp_region.x_id), Get_NAME_LENGTH((*R_INF), tmp_region.x_id)) == 0)
// &&
// (memcmp("m64016_190918_162737/130811282/ccs",
// Get_NAME((*R_INF), tmp_region.y_id), Get_NAME_LENGTH((*R_INF), tmp_region.y_id)) == 0)))
// {
// fprintf(stderr, "****************x_name: %.*s****************\n",
// Get_NAME_LENGTH((*R_INF), tmp_region.x_id), Get_NAME((*R_INF), tmp_region.x_id));
// fprintf(stderr, "****************y_name: %.*s****************\n",
// Get_NAME_LENGTH((*R_INF), tmp_region.y_id), Get_NAME((*R_INF), tmp_region.y_id));
// k_mer_hit* k_list = candidates->list + sub_region_beg;
// long long k_listLen = sub_region_end - sub_region_beg + 1;
// long long k = 0;
// fprintf(stderr, "k_listLen: %d\n", k_listLen);
// for (k = 0; k < k_listLen; k++)
// {
// fprintf(stderr, "k: %d, readID: %d, strand: %d, offset: %d, self_offset: %d\n",
// k, k_list[k].readID, k_list[k].strand, k_list[k].offset, k_list[k].self_offset);
// }
// }
chain_DP(candidates->list + sub_region_beg,
sub_region_end - sub_region_beg + 1, &(candidates->chainDP), &tmp_region, band_width_threshold,
50, Get_READ_LENGTH((*R_INF), tmp_region.x_id), Get_READ_LENGTH((*R_INF), tmp_region.y_id));
// if(
// ((memcmp("m64016_190918_162737/130811282/ccs",
// Get_NAME((*R_INF), tmp_region.x_id), Get_NAME_LENGTH((*R_INF), tmp_region.x_id)) == 0)
// &&
// (memcmp("m64016_190918_162737/179635219/ccs",
// Get_NAME((*R_INF), tmp_region.y_id), Get_NAME_LENGTH((*R_INF), tmp_region.y_id)) == 0))
// ||
// ((memcmp("m64016_190918_162737/179635219/ccs",
// Get_NAME((*R_INF), tmp_region.x_id), Get_NAME_LENGTH((*R_INF), tmp_region.x_id)) == 0)
// &&
// (memcmp("m64016_190918_162737/130811282/ccs",
// Get_NAME((*R_INF), tmp_region.y_id), Get_NAME_LENGTH((*R_INF), tmp_region.y_id)) == 0)))
// {
// fprintf(stderr, "****************x_name: %.*s****************\n",
// Get_NAME_LENGTH((*R_INF), tmp_region.x_id), Get_NAME((*R_INF), tmp_region.x_id));
// fprintf(stderr, "****************y_name: %.*s****************\n",
// Get_NAME_LENGTH((*R_INF), tmp_region.y_id), Get_NAME((*R_INF), tmp_region.y_id));
// k_mer_hit* k_list = candidates->list + sub_region_beg;
// long long k_listLen = sub_region_end - sub_region_beg + 1;
// long long k = 0;
// fprintf(stderr, "k_listLen: %d\n", k_listLen);
// for (k = 0; k < k_listLen; k++)
// {
// fprintf(stderr, "k: %d, score: %d, pre: %d, indels: %d, self_length: %d\n",
// k, candidates->chainDP.score[k], candidates->chainDP.pre[k],
// candidates->chainDP.indels[k], candidates->chainDP.self_length[k]);
// }
// }
///自己和自己重叠的要排除
///if (tmp_region.x_id != tmp_region.y_id && tmp_region.shared_seed > 1)
if (tmp_region.x_id != tmp_region.y_id)
{
///append_overlap_region_alloc(overlap_list, &tmp_region, R_INF);
/**
if(append_inexact_overlap_region_alloc(overlap_list, &tmp_region, R_INF))
{
debug_seed_offset(candidates->list + sub_region_beg,
sub_region_end - sub_region_beg + 1,
&(candidates->chainDP), &(overlap_list->list[overlap_list->length - 1]), R_INF);
}
**/
append_inexact_overlap_region_alloc(overlap_list, &tmp_region, R_INF);
}
}
destory_fake_cigar(&(tmp_region.f_cigar));
qsort(overlap_list->list, overlap_list->length, sizeof(overlap_region), cmp_by_x_pos_s);
}
void calculate_inexact_overlap_region(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF)
{
overlap_region tmp_region;
uint64_t i = 0;
long long current_pos_diff;
long long current_self_pos;
uint64_t current_ID;
uint64_t current_stand;
long long tmp_pos_distance;
long long tmp_self_pos_distance;
long long constant_distance = 5;
double error_rate = 0.05;
if (candidates->length == 0)
{
return;
}
i = 0;
while (i < candidates->length)
{
current_pos_diff = candidates->list[i].offset - candidates->list[i].self_offset;
current_self_pos = candidates->list[i].self_offset;
current_ID = candidates->list[i].readID;
current_stand = candidates->list[i].strand;
tmp_region.shared_seed = 1;
///这个是查询read的信息
tmp_region.x_id = readID;
tmp_region.x_pos_s = candidates->list[i].self_offset;
tmp_region.x_pos_e = candidates->list[i].self_offset;
tmp_region.x_pos_strand = current_stand;
///这个是被查询的read的信息
tmp_region.y_id = current_ID;
tmp_region.y_pos_s = candidates->list[i].offset;
tmp_region.y_pos_e = candidates->list[i].offset;
tmp_region.y_pos_strand = 0; ///永远是0
// if(memcmp("m64013_190412_043951/159056664/ccs", Get_NAME((*R_INF), readID),
// Get_NAME_LENGTH((*R_INF), readID)) == 0
// &&
// memcmp("m64013_190322_203854/42402522/ccs", Get_NAME((*R_INF), current_ID),
// Get_NAME_LENGTH((*R_INF), current_ID)) == 0)
// {
// fprintf(stderr, "***********i: %d, x_pos_s: %d, x_pos_e: %d, y_pos_s: %d, y_pos_e: %d\n",
// i, tmp_region.x_pos_s, tmp_region.x_pos_e, tmp_region.y_pos_s, tmp_region.y_pos_e);
// fprintf(stderr, "***********i: %d, self_offset: %d, offset: %d\n",
// i, candidates->list[i].self_offset, candidates->list[i].offset);
// }
i++;
while (i < candidates->length)
{
if (current_ID == candidates->list[i].readID &&
current_stand == candidates->list[i].strand)
{
///这个一定是正值
tmp_pos_distance = candidates->list[i].offset - candidates->list[i].self_offset - current_pos_diff;
///这个不一定是正值
tmp_self_pos_distance = candidates->list[i].self_offset - current_self_pos;
if(tmp_self_pos_distance < 0)
{
///fprintf(stderr, "tmp_self_pos_distance: %d\n", tmp_self_pos_distance);
tmp_self_pos_distance = tmp_self_pos_distance * -1;
///fprintf(stderr, "tmp_self_pos_distance: %d\n", tmp_self_pos_distance);
}
///if (tmp_self_pos_distance >= 0)
{
tmp_self_pos_distance = tmp_self_pos_distance * error_rate + constant_distance;
if (tmp_pos_distance < tmp_self_pos_distance)
{
/****************************may have bugs********************************/
///i++;
// tmp_region.x_pos_e = candidates->list[i].self_offset;
// tmp_region.y_pos_e = candidates->list[i].offset;
/****************************may have bugs********************************/
tmp_region.shared_seed++;
if(candidates->list[i].self_offset < tmp_region.x_pos_s)
{
tmp_region.x_pos_s = candidates->list[i].self_offset;
}
if(candidates->list[i].self_offset > tmp_region.x_pos_e)
{
tmp_region.x_pos_e = candidates->list[i].self_offset;
}
if(candidates->list[i].offset < tmp_region.y_pos_s)
{
tmp_region.y_pos_s = candidates->list[i].offset;
}
if(candidates->list[i].offset > tmp_region.y_pos_e)
{
tmp_region.y_pos_e = candidates->list[i].offset;
}
// if(memcmp("m64013_190412_043951/159056664/ccs", Get_NAME((*R_INF), readID),
// Get_NAME_LENGTH((*R_INF), readID)) == 0
// &&
// memcmp("m64013_190322_203854/42402522/ccs", Get_NAME((*R_INF), current_ID),
// Get_NAME_LENGTH((*R_INF), current_ID)) == 0)
// {
// fprintf(stderr, "i: %d, x_pos_s: %d, x_pos_e: %d, y_pos_s: %d, y_pos_e: %d\n",
// i, tmp_region.x_pos_s, tmp_region.x_pos_e, tmp_region.y_pos_s, tmp_region.y_pos_e);
// fprintf(stderr, "i: %d, self_offset: %d, offset: %d, tmp_pos_distance: %d, tmp_self_pos_distance: %d\n",
// i, candidates->list[i].self_offset, candidates->list[i].offset, tmp_pos_distance,
// tmp_self_pos_distance);
// }
/****************************may have bugs********************************/
i++;
/****************************may have bugs********************************/
continue;
}
}
}
break;
}
///自己和自己重叠的要排除
///if (tmp_region.x_id != tmp_region.y_id && tmp_region.shared_seed > 1)
if (tmp_region.x_id != tmp_region.y_id)
{
append_inexact_overlap_region_alloc(overlap_list, &tmp_region, R_INF);
}
}
}
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
int extra_begin, int extra_end, int error_threshold)
{
long long length = region->x_pos_e - region->x_pos_s + 1;
///the length of window may large or small than WINDOW
/****************************may have bugs********************************/
long long num_windows = length / WINDOW + 4;
/****************************may have bugs********************************/
///w_list_length会在clear_overlap_region_alloc中定时清空
if (num_windows > region->w_list_size)
{
region->w_list_size = num_windows;
region->w_list = (window_list*)realloc(region->w_list, region->w_list_size*sizeof(window_list));
}
region->w_list[region->w_list_length].x_start = x_start;
region->w_list[region->w_list_length].x_end = x_end;
region->w_list[region->w_list_length].y_start = y_start;
region->w_list[region->w_list_length].y_end = y_end;
region->w_list[region->w_list_length].error = error;
region->w_list[region->w_list_length].cigar.length = -1;
region->w_list[region->w_list_length].extra_begin = extra_begin;
region->w_list[region->w_list_length].extra_end = extra_end;
region->w_list[region->w_list_length].error_threshold = error_threshold;
region->w_list_length++;
}
void init_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
list->size = 1000;
list->length = 0;
//list->list = (k_mer_pos_list*)malloc(sizeof(k_mer_pos_list)*list->size);
list->list = (k_mer_pos_list*)calloc(list->size, sizeof(k_mer_pos_list));
}
void clear_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
list->length = 0;
}
void destory_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
free(list->list);
}
void append_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list, k_mer_pos* n_list, uint64_t n_length,
uint64_t n_end_pos, uint8_t n_direction)
{
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);
}
list->list[list->length].list = n_list;
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++;
}
int cmp_k_mer_pos_list(const void * a, const void * b)
{
if ((*(k_mer_pos_list*)a).length > (*(k_mer_pos_list*)b).length)
{
return 1;
}
else if ((*(k_mer_pos_list*)a).length < (*(k_mer_pos_list*)b).length)
{
return -1;
}
else
{
return 0;
}
}
inline void append_pos_to_Candidates_list(Candidates_list* candidates, ElemType* x)
{
candidates->list[candidates->length] = x->node;
candidates->length++;
}
void test_single_list(Candidates_list* candidates, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, uint64_t strand)
{
uint64_t i;
int j = 0;
for (i = 0; i < n_lengh; i++)
{
for (; j < candidates->length; j++)
{
if (
n_list[i].offset == candidates->list[j].offset
&&
n_list[i].readID == candidates->list[j].readID
&&
end_pos == candidates->list[j].self_offset
&&
strand == candidates->list[j].strand
)
{
break;
}
}
if (j == candidates->length)
{
fprintf(stderr, "ERROR 4\n");
}
}
}
void verify_merge_result(k_mer_pos_list_alloc* list, Candidates_list* candidates)
{
uint64_t total_length = 0;
uint64_t i = 0;
long long r_dis_x, r_dis_y;
for (i = 0; i < list->length; i++)
{
total_length = total_length + list->list[i].length;
}
if (total_length!=candidates->length)
{
fprintf(stderr, "ERROR length & size.\n");
}
for (i = 1; i < candidates->length; i++)
{
if (candidates->list[i].strand < candidates->list[i-1].strand)
{
fprintf(stderr, "ERROR -1\n");
}
else if (candidates->list[i].strand == candidates->list[i-1].strand)
{
if (candidates->list[i].readID < candidates->list[i-1].readID)
{
fprintf(stderr, "ERROR 0\n");
}
else if (candidates->list[i].readID == candidates->list[i-1].readID)
{
r_dis_x = candidates->list[i].offset - candidates->list[i].self_offset;
r_dis_y = candidates->list[i-1].offset - candidates->list[i-1].self_offset;
///if (candidates->list[i].offset < candidates->list[i-1].offset)
if (r_dis_x < r_dis_y)
{
fprintf(stderr, "ERROR 1\n");
}
///else if (candidates->list[i].offset == candidates->list[i-1].offset)
else if (r_dis_x == r_dis_y)
{
if (candidates->list[i].self_offset < candidates->list[i-1].self_offset)
{
fprintf(stderr, "ERROR 2\n");
}
}
}
}
}
uint64_t j = 0;
for (i = 0; i < list->length; i++)
{
test_single_list(candidates, list->list[i].list, list->list[i].length, list->list[i].end_pos, list->list[i].direction);
}
}
void output_to_stderr(Candidates_list* candidates)
{
uint64_t i = 0;
pthread_mutex_lock(&output_mutex);
fprintf(stderr, "************************\nLength: %llu\n", candidates->length);
for (i = 0; i < candidates->length; i++)
{
fprintf(stderr, "\ni: %llu\n", i);
fprintf(stderr, "strand: %llu\n", candidates->list[i].strand);
fprintf(stderr, "readID: %llu\n", candidates->list[i].readID);
fprintf(stderr, "diff: %lld\n", candidates->list[i].offset - candidates->list[i].self_offset);
fprintf(stderr, "offset: %lld\n", candidates->list[i].offset);
fprintf(stderr, "self_offset: %lld\n", candidates->list[i].self_offset);
}
pthread_mutex_unlock(&output_mutex);
}
void merge_k_mer_pos_list_alloc_heap_sort_back(k_mer_pos_list_alloc* list, Candidates_list* candidates, HeapSq* HBT)
{
clear_Heap(HBT);
uint64_t total_length = 0;
uint64_t i;
ElemType x, y;
///所有list的长度都不是0
///把各个表第一个元素加入到堆中
for (i = 0; i < list->length; i++)
{
x.ID = i;
x.node.offset = list->list[i].list[0].offset;
x.node.readID = list->list[i].list[0].readID;
x.node.self_offset = list->list[i].end_pos;
x.node.strand = list->list[i].direction;
Insert_Heap(HBT, &x);
HBT->index_i[i] = 1;
total_length = total_length + list->list[i].length;
}
candidates->length = 0;
if(total_length > candidates->size)
{
candidates->size = total_length;
candidates->list = (k_mer_hit*)realloc(candidates->list, sizeof(k_mer_hit)*candidates->size);
candidates->tmp = (k_mer_hit*)realloc(candidates->tmp, sizeof(k_mer_hit)*candidates->size);
}
uint64_t ID;
while (DeleteHeap(HBT, &x))
{
append_pos_to_Candidates_list(candidates, &x);
///x.ID说明是从第x.ID个列表中的这个节点已经从堆里出来了
///HBT->index_i[x.ID]是第x.ID个列表的当前元素的下标
i = HBT->index_i[x.ID];
ID = x.ID;
///fprintf(stderr, "x.ID: %llu, i: %llu, length: %llu\n", x.ID, i, list->list[x.ID].length);
if (i < list->list[x.ID].length)
{
y.ID = ID;
y.node.offset = list->list[x.ID].list[i].offset;
y.node.readID = list->list[x.ID].list[i].readID;
y.node.self_offset = list->list[x.ID].end_pos;
y.node.strand = list->list[x.ID].direction;
Insert_Heap(HBT, &y);
HBT->index_i[ID]++;
}
}
///verify_merge_result(list, candidates);
}
void merge_k_mer_pos_list_alloc_heap_sort(k_mer_pos_list_alloc* list, Candidates_list* candidates, HeapSq* HBT)
{
clear_Heap(HBT);
uint64_t total_length = 0;
uint64_t i;
ElemType x, y;
///所有list的长度都不是0
///把各个表第一个元素加入到堆中
for (i = 0; i < list->length; i++)
{
x.ID = i;
x.node.offset = list->list[i].list[0].offset;
x.node.readID = list->list[i].list[0].readID;
x.node.self_offset = list->list[i].end_pos;
x.node.strand = list->list[i].direction;
Insert_Heap(HBT, &x);
HBT->index_i[i] = 1;
total_length = total_length + list->list[i].length;
}
candidates->length = 0;
if(total_length > candidates->size)
{
candidates->size = total_length;
candidates->list = (k_mer_hit*)realloc(candidates->list, sizeof(k_mer_hit)*candidates->size);
candidates->tmp = (k_mer_hit*)realloc(candidates->tmp, sizeof(k_mer_hit)*candidates->size);
}
uint64_t ID;
int flag;
while (flag = DeleteHeap(HBT, &x))
{
append_pos_to_Candidates_list(candidates, &x);
///x.ID说明是从第x.ID个列表中的这个节点已经从堆里出来了
///HBT->index_i[x.ID]是第x.ID个列表的当前元素的下标
i = HBT->index_i[x.ID];
ID = x.ID;
if (flag == 2)
{
for (; i < list->list[x.ID].length; i++)
{
y.ID = ID;
y.node.offset = list->list[x.ID].list[i].offset;
y.node.readID = list->list[x.ID].list[i].readID;
y.node.self_offset = list->list[x.ID].end_pos;
y.node.strand = list->list[x.ID].direction;
append_pos_to_Candidates_list(candidates, &y);
}
break;
}
if (i < list->list[x.ID].length)
{
y.ID = ID;
y.node.offset = list->list[x.ID].list[i].offset;
y.node.readID = list->list[x.ID].list[i].readID;
y.node.self_offset = list->list[x.ID].end_pos;
y.node.strand = list->list[x.ID].direction;
Insert_Heap(HBT, &y);
HBT->index_i[ID]++;
}
}
///verify_merge_result(list, candidates);
///output_to_stderr(candidates);
}
void insert_kv_list_to_candidates(k_v* list, long long occ, long long y_id, long long y_offset, long long y_strand,
Candidates_list* candidates)
{
if(candidates->length + occ > candidates->size)
{
candidates->size = (candidates->length + occ) * 2;
candidates->list = (k_mer_hit*)realloc(candidates->list, sizeof(k_mer_hit)*candidates->size);
candidates->tmp = (k_mer_hit*)realloc(candidates->tmp, sizeof(k_mer_hit)*candidates->size);
}
long long i;
ElemType x;
for (i = 0; i < occ; i++)
{
x.node.offset = y_offset;
x.node.readID = y_id;
x.node.self_offset = list[i].value;
x.node.strand = y_strand;
append_pos_to_Candidates_list(candidates, &x);
}
}
///有bug，找时间排一下
void merge_k_mer_pos_list_alloc_heap_sort_advance(k_mer_pos_list_alloc* list, Candidates_list* candidates, HeapSq* HBT)
{
uint64_t total_length = 0;
uint64_t i;
ElemType x, y;
/************************************forward*************************************************/
clear_Heap(HBT);
///所有list的长度都不是0
///把各个表第一个元素加入到堆中
for (i = 0; i < list->length; i++)
{
if (list->list[i].direction == 0)
{
x.ID = i;
x.node.offset = list->list[i].list[0].offset;
x.node.readID = list->list[i].list[0].readID;
x.node.self_offset = list->list[i].end_pos;
x.node.strand = list->list[i].direction;
Insert_Heap(HBT, &x);
HBT->index_i[i] = 1;
total_length = total_length + list->list[i].length;
}
}
candidates->length = 0;
if(total_length > candidates->size)
{
candidates->size = total_length;
candidates->list = (k_mer_hit*)realloc(candidates->list, sizeof(k_mer_hit)*candidates->size);
candidates->tmp = (k_mer_hit*)realloc(candidates->tmp, sizeof(k_mer_hit)*candidates->size);
}
uint64_t ID;
int flag;
while (flag = DeleteHeap(HBT, &x))
{
append_pos_to_Candidates_list(candidates, &x);
///x.ID说明是从第x.ID个列表中的这个节点已经从堆里出来了
///HBT->index_i[x.ID]是第x.ID个列表的当前元素的下标
i = HBT->index_i[x.ID];
ID = x.ID;
///fprintf(stderr, "x.ID: %llu, i: %llu, length: %llu\n", x.ID, i, list->list[x.ID].length);
/**
if (flag == 2)
{
for (; i < list->list[x.ID].length; i++)
{
y.ID = ID;
y.node.offset = list->list[x.ID].list[i].offset;
y.node.readID = list->list[x.ID].list[i].readID;
y.node.self_offset = list->list[x.ID].end_pos;
y.node.strand = list->list[x.ID].direction;
append_pos_to_Candidates_list(candidates, &y);
}
break;
}
**/
if (i < list->list[x.ID].length)
{
y.ID = ID;
y.node.offset = list->list[x.ID].list[i].offset;
y.node.readID = list->list[x.ID].list[i].readID;
y.node.self_offset = list->list[x.ID].end_pos;
y.node.strand = list->list[x.ID].direction;
Insert_Heap(HBT, &y);
HBT->index_i[ID]++;
}
}
/************************************reverse complement*************************************************/
clear_Heap(HBT);
///所有list的长度都不是0
///把各个表第一个元素加入到堆中
for (i = 0; i < list->length; i++)
{
if (list->list[i].direction == 1)
{
x.ID = i;
x.node.offset = list->list[i].list[0].offset;
x.node.readID = list->list[i].list[0].readID;
x.node.self_offset = list->list[i].end_pos;
x.node.strand = list->list[i].direction;
Insert_Heap(HBT, &x);
HBT->index_i[i] = 1;
total_length = total_length + list->list[i].length;
}
}
if(total_length > candidates->size)
{
candidates->size = total_length;
candidates->list = (k_mer_hit*)realloc(candidates->list, sizeof(k_mer_hit)*candidates->size);
candidates->tmp = (k_mer_hit*)realloc(candidates->tmp, sizeof(k_mer_hit)*candidates->size);
}
while (flag = DeleteHeap(HBT, &x))
{
append_pos_to_Candidates_list(candidates, &x);
///x.ID说明是从第x.ID个列表中的这个节点已经从堆里出来了
///HBT->index_i[x.ID]是第x.ID个列表的当前元素的下标
i = HBT->index_i[x.ID];
ID = x.ID;
///fprintf(stderr, "x.ID: %llu, i: %llu, length: %llu\n", x.ID, i, list->list[x.ID].length);
/**
if (flag == 2)
{
for (; i < list->list[x.ID].length; i++)
{
y.ID = ID;
y.node.offset = list->list[x.ID].list[i].offset;
y.node.readID = list->list[x.ID].list[i].readID;
y.node.self_offset = list->list[x.ID].end_pos;
y.node.strand = list->list[x.ID].direction;
append_pos_to_Candidates_list(candidates, &y);
}
break;
}
**/
if (i < list->list[x.ID].length)
{
y.ID = ID;
y.node.offset = list->list[x.ID].list[i].offset;
y.node.readID = list->list[x.ID].list[i].readID;
y.node.self_offset = list->list[x.ID].end_pos;
y.node.strand = list->list[x.ID].direction;
Insert_Heap(HBT, &y);
HBT->index_i[ID]++;
}
}
}
void merge_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list, Candidates_list* candidates)
{
qsort(list->list, list->length, sizeof(k_mer_pos_list), cmp_k_mer_pos_list);
uint64_t i;
for (i = 0; i < list->length; i++)
{
/**
if (i > 0 && (list->list[i].length < list->list[i-1].length || list->list[i].length == 0 || list->list[i-1].length == 0))
{
fprintf(stderr, "ERROR\n");
}
**/
merge_Candidates_list(candidates, list->list[i].list, list->list[i].length,
list->list[i].end_pos, list->list[i].direction);
}
}
void init_Count_Table(Count_Table** table)
{
*table = kh_init(COUNT64);
}
void init_Pos_Table(Pos_Table** table)
{
*table = kh_init(POS64);
}
void init_Total_Count_Table(int k, Total_Count_Table* TCB)
{
if(k>64)
{
fprintf(stdout, "k-mer is too long. The length of k-mer must <= 64.");
fflush(stdout);
exit(0);
}
int total_bits = k * 2;
TCB->prefix_bits = PREFIX_BITS;
TCB->suffix_bits = total_bits - TCB->prefix_bits;
if (TCB->suffix_bits > MAX_SUFFIX_BITS)
{
TCB->suffix_bits = MAX_SUFFIX_BITS;
TCB->prefix_bits = total_bits - TCB->suffix_bits;
}
///TCB->suffix_mode = (1ULL<<TCB->suffix_bits) - 1;
///这个右移是安全的，因为TCB->suffix_bits不可能是0
TCB->suffix_mode = ALL >> (64 - TCB->suffix_bits);
///number of small hash table
TCB->size = (1ULL<<TCB->prefix_bits);
TCB->sub_h = (Count_Table**)malloc(sizeof(Count_Table*)*TCB->size);
TCB->sub_h_lock = (Hash_table_spin_lock*)malloc(sizeof(Hash_table_spin_lock)*TCB->size);
memset(TCB->sub_h_lock, 0, sizeof(Hash_table_spin_lock)*TCB->size);
int i = 0;
for (i = 0; i < TCB->size; i++)
{
init_Count_Table(&(TCB->sub_h[i]));
TCB->sub_h_lock[i].lock = 0;
}
TCB->non_unique_k_mer = 0;
}
void init_Total_Pos_Table(Total_Pos_Table* TCB, Total_Count_Table* pre_TCB)
{
TCB->prefix_bits = pre_TCB->prefix_bits;
TCB->suffix_bits = pre_TCB->suffix_bits;
TCB->suffix_mode = pre_TCB->suffix_mode;
TCB->size = pre_TCB->size;
TCB->useful_k_mer = 0;
TCB->total_occ = 0;
TCB->k_mer_index = NULL;
TCB->sub_h_lock = (Hash_table_spin_lock*)malloc(sizeof(Hash_table_spin_lock)*TCB->size);
memset(TCB->sub_h_lock, 0, sizeof(Hash_table_spin_lock)*TCB->size);
TCB->sub_h = (Pos_Table**)malloc(sizeof(Pos_Table*)*TCB->size);
TCB->pos = NULL;
int i = 0;
for (i = 0; i < TCB->size; i++)
{
init_Pos_Table(&(TCB->sub_h[i]));
TCB->sub_h_lock[i].lock = 0;
}
}
void destory_Total_Count_Table(Total_Count_Table* TCB)
{
int i;
for (i = 0; i < TCB->size; i++)
{
kh_destroy(COUNT64, TCB->sub_h[i]);
}
free(TCB->sub_h);
free(TCB->sub_h_lock);
}
void destory_Total_Pos_Table(Total_Pos_Table* TCB)
{
free(TCB->k_mer_index);
free(TCB->sub_h_lock);
free(TCB->pos);
int i;
for (i = 0; i < TCB->size; i++)
{
kh_destroy(POS64, TCB->sub_h[i]);
}
free(TCB->sub_h);
}
void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
{
fprintf(stdout, "Writing index to disk ...... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+5);
sprintf(index_name, "%s.idx", read_file_name);
FILE* fp = fopen(index_name, "w");
fwrite(&adapterLen, sizeof(adapterLen), 1, fp);
fwrite(&k_mer_min_freq, sizeof(k_mer_min_freq), 1, fp);
fwrite(&k_mer_max_freq, sizeof(k_mer_max_freq), 1, fp);
fwrite(&TCB->prefix_bits, sizeof(TCB->prefix_bits), 1, fp);
fwrite(&TCB->suffix_bits, sizeof(TCB->suffix_bits), 1, fp);
fwrite(&TCB->suffix_mode, sizeof(TCB->suffix_mode), 1, fp);
fwrite(&TCB->size, sizeof(TCB->size), 1, fp);
fwrite(&TCB->useful_k_mer, sizeof(TCB->useful_k_mer), 1, fp);
fwrite(&TCB->total_occ, sizeof(TCB->total_occ), 1, fp);
fwrite(TCB->k_mer_index, sizeof(uint64_t), TCB->useful_k_mer+1, fp);
fwrite(TCB->pos, sizeof(k_mer_pos), TCB->total_occ, fp);
int i;
for (i = 0; i < TCB->size; i++)
{
kh_write(POS64, TCB->sub_h[i], fp);
}
free(index_name);
fclose(fp);
fprintf(stdout, "Index has been written.\n");
}
int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
{
fprintf(stdout, "Loading index to disk ...... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+5);
sprintf(index_name, "%s.idx", read_file_name);
FILE* fp = fopen(index_name, "r");
if (!fp)
{
return 0;
}
int local_adapterLen;
fread(&local_adapterLen, sizeof(local_adapterLen), 1, fp);
if(local_adapterLen != adapterLen)
{
fprintf(stdout, "the adapterLen of index is: %d, but the adapterLen set by user is: %d\n",
local_adapterLen, adapterLen);
exit(1);
}
fread(&k_mer_min_freq, sizeof(k_mer_min_freq), 1, fp);
fread(&k_mer_max_freq, sizeof(k_mer_max_freq), 1, fp);
fread(&TCB->prefix_bits, sizeof(TCB->prefix_bits), 1, fp);
fread(&TCB->suffix_bits, sizeof(TCB->suffix_bits), 1, fp);
fread(&TCB->suffix_mode, sizeof(TCB->suffix_mode), 1, fp);
fread(&TCB->size, sizeof(TCB->size), 1, fp);
fread(&TCB->useful_k_mer, sizeof(TCB->useful_k_mer), 1, fp);
fread(&TCB->total_occ, sizeof(TCB->total_occ), 1, fp);
if (TCB->useful_k_mer+1)
{
TCB->k_mer_index = (uint64_t*)malloc(sizeof(uint64_t)*(TCB->useful_k_mer+1));
fread(TCB->k_mer_index, sizeof(uint64_t), TCB->useful_k_mer+1, fp);
}
else
{
TCB->k_mer_index = NULL;
}
if (TCB->total_occ)
{
TCB->pos = (k_mer_pos*)malloc(sizeof(k_mer_pos)*TCB->total_occ);
fread(TCB->pos, sizeof(k_mer_pos), TCB->total_occ, fp);
}
else
{
TCB->pos = NULL;
}
TCB->sub_h_lock = (Hash_table_spin_lock*)malloc(sizeof(Hash_table_spin_lock)*TCB->size);
memset(TCB->sub_h_lock, 0, sizeof(Hash_table_spin_lock)*TCB->size);
TCB->sub_h = (Pos_Table**)malloc(sizeof(Pos_Table*)*TCB->size);
int i;
for (i = 0; i < TCB->size; i++)
{
init_Pos_Table(&(TCB->sub_h[i]));
TCB->sub_h_lock[i].lock = 0;
kh_load(POS64, TCB->sub_h[i], fp);
}
free(index_name);
fclose(fp);
fprintf(stdout, "Index has been loaded.\n");
return 1;
}
void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k_mer_min_freq, int k_mer_max_freq)
{
int i;
Count_Table* h;
khint_t k;
uint64_t sub_key;
uint64_t sub_ID;
PCB->useful_k_mer = 0;
PCB->total_occ = 0;
///init_Total_Pos_Table(PCB, TCB);
khint_t t; ///这就是个迭代器
int absent;
/********************************************
hash_table(key) ----> PCB->k_mer_index ------> PCB->pos
********************************************/
for (i = 0; i < TCB->size; i++)
{
h = TCB->sub_h[i];
for (k = kh_begin(h); k != kh_end(h); ++k)
{
if (kh_exist(h, k)) // test if a bucket contains data
{
///只有符合频率范围要求的k-mer，才会被加入到pos table中
if (kh_value(h, k)>=k_mer_min_freq && kh_value(h, k)<=k_mer_max_freq)
{
sub_ID = i;
sub_key = kh_key(h, k);
t = kh_put(POS64, PCB->sub_h[sub_ID], sub_key, &absent);
if (absent)
{
///kh_value(PCB->sub_h[sub_ID], t) = useful_k_mer + total_occ;
kh_value(PCB->sub_h[sub_ID], t) = PCB->useful_k_mer;
}
else ///哈希表中已有的元素
{
///kh_value(PCB->sub_h[sub_ID], t)++;
fprintf(stderr, "ERROR\n");
}
PCB->useful_k_mer++;
PCB->total_occ = PCB->total_occ + kh_value(h, k);
}
}
}
}
fprintf(stdout, "useful_k_mer: %lld\n",PCB->useful_k_mer);
fprintf(stdout, "total_occ: %lld\n",PCB->total_occ);
PCB->k_mer_index = (uint64_t*)malloc(sizeof(uint64_t)*(PCB->useful_k_mer+1));
PCB->k_mer_index[0] = 0;
PCB->total_occ = 0;
PCB->useful_k_mer = 0;
for (i = 0; i < TCB->size; i++)
{
h = TCB->sub_h[i];
for (k = kh_begin(h); k != kh_end(h); ++k)
{
if (kh_exist(h, k)) // test if a bucket contains data
{
if (kh_value(h, k)>=k_mer_min_freq && kh_value(h, k)<=k_mer_max_freq)
{
PCB->useful_k_mer++;
PCB->total_occ = PCB->total_occ + kh_value(h, k);
PCB->k_mer_index[PCB->useful_k_mer] = PCB->total_occ;
}
}
}
}
PCB->pos = (k_mer_pos*)malloc(sizeof(k_mer_pos)*PCB->total_occ);
memset(PCB->pos, 0, sizeof(k_mer_pos)*PCB->total_occ);
}
int cmp_k_mer_pos(const void * a, const void * b)
{
if ((*(k_mer_pos*)a).readID != (*(k_mer_pos*)b).readID)
{
return (*(k_mer_pos*)a).readID > (*(k_mer_pos*)b).readID ? 1 : -1;
}
else
{
if ((*(k_mer_pos*)a).offset != (*(k_mer_pos*)b).offset)
{
return (*(k_mer_pos*)a).offset > (*(k_mer_pos*)b).offset ? 1 : -1;
}
else
{
return 0;
}
}
}
void init_Chain_Data(Chain_Data* x)
{
x->length = 0;
x->size = 0;
x->score = NULL;
x->pre = NULL;
x->indels = NULL;
x->self_length = NULL;
}
void clear_Chain_Data(Chain_Data* x)
{
x->length = 0;
}
void destory_Chain_Data(Chain_Data* x)
{
free(x->score);
free(x->pre);
free(x->indels);
free(x->self_length);
}
void resize_Chain_Data(Chain_Data* x, long long size)
{
if(size > x->size)
{
x->size = size;
x->score = (long long*)realloc(x->score, x->size*sizeof(long long));
x->pre = (long long*)realloc(x->pre, x->size*sizeof(long long));
x->indels = (long long*)realloc(x->indels, x->size*sizeof(long long));
x->self_length = (long long*)realloc(x->self_length, x->size*sizeof(long long));
}
}
void init_Candidates_list(Candidates_list* l)
{
l->length = 0;
l->size = 0;
l->list = NULL;
l->tmp = NULL;
l->foward_pos = 0;
l->rc_pos = 0;
init_Chain_Data(&(l->chainDP));
}
void clear_Candidates_list(Candidates_list* l)
{
l->length = 0;
l->foward_pos = 0;
l->rc_pos = 0;
clear_Chain_Data(&(l->chainDP));
}
void destory_Candidates_list(Candidates_list* l)
{
free(l->list);
free(l->tmp);
destory_Chain_Data(&(l->chainDP));
}
///1是x小，2是y小，0是相等
inline int cmp_pos(k_mer_hit* x, k_mer_pos* y, uint64_t y_pos, uint8_t strand)
{
if (x->strand < strand)
{
return 1;
}
else if (x->strand > strand)
{
return 2;
}
else
{
if (x->readID < y->readID)
{
return 1;
}
else if (x->readID > y->readID)
{
return 2;
}
else
{
if (x->offset < y->offset)
{
return 1;
}
else if (x->offset > y->offset)
{
return 2;
}
else
{
if (x->self_offset < y_pos)
{
return 1;
}
else if (x->self_offset > y_pos)
{
return 2;
}
else
{
return 0;
}
}
}
}
}
void debug_merge_Candidates_list(Candidates_list* l, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, uint64_t i,
uint64_t i_1, uint64_t i_2, uint64_t len1, uint64_t len2, uint64_t strand)
{
if (i != l->length)
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "i: %llu, l->length: %llu\n", i , l->length);
fprintf(stderr, "i_1: %llu, len1: %llu\n", i_1 , len1);
fprintf(stderr, "i_2: %llu, len2: %llu\n", i_2 , len2);
fprintf(stderr, "strand: %llu\n", strand);
}
for (i = 1; i < l->length; i++)
{
if (l->list[i].strand < l->list[i-1].strand)
{
fprintf(stderr, "ERROR -1\n");
}
else if (l->list[i].strand == l->list[i-1].strand)
{
if (l->list[i].readID < l->list[i-1].readID)
{
fprintf(stderr, "ERROR 0\n");
}
else if (l->list[i].readID == l->list[i-1].readID)
{
if (l->list[i].offset < l->list[i-1].offset)
{
fprintf(stderr, "ERROR 1\n");
}
else if (l->list[i].offset == l->list[i-1].offset)
{
if (l->list[i].self_offset < l->list[i-1].self_offset)
{
fprintf(stderr, "ERROR 2\n");
}
}
}
}
}
for (i = 0; i < n_lengh; i++)
{
int j = 0;
for (j = 0; j < l->length; j++)
{
if (
n_list[i].offset == l->list[j].offset
&&
n_list[i].readID == l->list[j].readID
&&
end_pos == l->list[j].self_offset
&&
strand == l->list[j].strand
)
{
break;
}
}
if (j == l->length)
{
fprintf(stderr, "ERROR 4\n");
}
}
for (i = 0; i < l->length - n_lengh; i++)
{
int j = 0;
for (j = 0; j < l->length; j++)
{
if (
l->tmp[i].offset == l->list[j].offset
&&
l->tmp[i].readID == l->list[j].readID
&&
l->tmp[i].self_offset == l->list[j].self_offset
&&
l->tmp[i].strand == l->list[j].strand
)
{
break;
}
}
if (j == l->length)
{
fprintf(stderr, "ERROR 5\n");
}
}
}
void merge_Candidates_list(Candidates_list* l, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, int strand)
{
if (n_lengh == 0) ///不加这个就会巨慢
{
return;
}
if(l->length + n_lengh > l->size)
{
l->size = l->length + n_lengh;
l->list = (k_mer_hit*)realloc(l->list, sizeof(k_mer_hit)*l->size);
l->tmp = (k_mer_hit*)realloc(l->tmp, sizeof(k_mer_hit)*l->size);
}
int flag;
uint64_t len1, len2, i_1, i_2, i;
k_mer_hit *l_1;
k_mer_pos *l_2;
l_1 = l->list;
if (strand == 0)
{
///由于标号全是0，则标号为1的位置不受影响(数组后半部分)，可以直接复制过去
///需要从l_1 + l->rc_pos开始，复制l->length-l->rc_pos个元素，到l->tmp + l->rc_pos + n_lengh处
memcpy(l->tmp + l->rc_pos + n_lengh, l_1 + l->rc_pos, sizeof(k_mer_hit)*(l->length-l->rc_pos));
///l_1只需要从0扫描到l->rc_pos就好了
len1 = l->rc_pos;
i_1 = 0;
///此时目标数组没数据，
i = 0;
///更新l->rc_pos
l->rc_pos = l->rc_pos + n_lengh;
}
else
{
///如果strand==1，则标号为0的位置不受影响(数组前半部分)，可以直接复制过去
///从l_1开始，复制l->rc_pos个元素，到l->tmp
memcpy(l->tmp, l_1, sizeof(k_mer_hit)*l->rc_pos);
///l_1只需要从l->rc_pos扫描到末尾就好了
i_1 = l->rc_pos;
len1 = l->length;
///此时目标数组已经有了l->rc_pos
i = i_1;
///l->rc_pos不用更新
}
l_2 = n_list;
len2 = n_lengh;
i_2 = 0;
while (i_1<len1 && i_2<len2)
{
flag = cmp_pos(&l_1[i_1], &l_2[i_2], end_pos, strand);
///l_1小
if (flag == 1)
{
l->tmp[i].readID = l_1[i_1].readID;
l->tmp[i].offset = l_1[i_1].offset;
l->tmp[i].self_offset = l_1[i_1].self_offset;
l->tmp[i].strand = l_1[i_1].strand;
i_1++;
i++;
}
else ///l_2小或者l_1 == l_2
{
l->tmp[i].readID = l_2[i_2].readID;
l->tmp[i].offset = l_2[i_2].offset;
l->tmp[i].self_offset = end_pos;
l->tmp[i].strand = strand;
i_2++;
i++;
}
}
while (i_1<len1)
{
memcpy(l->tmp + i, l_1 + i_1, sizeof(k_mer_hit)*(len1-i_1));
i = i + len1-i_1;
i_1 = len1;
}
while (i_2<len2)
{
l->tmp[i].readID = l_2[i_2].readID;
l->tmp[i].offset = l_2[i_2].offset;
l->tmp[i].self_offset = end_pos;
l->tmp[i].strand = strand;
i_2++;
i++;
}
k_mer_hit* k;
k = l->list;
l->list = l->tmp;
l->tmp = k;
l->length = l->length + n_lengh;
/**
if (strand == 0)
{
i = l->length;
len1 = l->length - n_lengh;
}
debug_merge_Candidates_list(l, n_list, n_lengh, end_pos, i, i_1, i_2, len1, len2, strand);
**/
}
/********************************for debug***************************************/
void merge_Candidates_list_version(Candidates_list* l, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, int strand)
{
if (n_lengh == 0) ///不加这个就会巨慢
{
return;
}
if(l->length + n_lengh > l->size)
{
l->size = l->length + n_lengh;
l->list = (k_mer_hit*)realloc(l->list, sizeof(k_mer_hit)*l->size);
l->tmp = (k_mer_hit*)realloc(l->tmp, sizeof(k_mer_hit)*l->size);
}
int flag;
uint64_t len1, len2, i_1, i_2, i;
k_mer_hit *l_1;
k_mer_pos *l_2;
l_1 = l->list;
len1 = l->length;
i_1 = 0;
l_2 = n_list;
len2 = n_lengh;
i_2 = 0;
i = 0;
while (i_1<len1 && i_2<len2)
{
flag = cmp_pos(&l_1[i_1], &l_2[i_2], end_pos, strand);
///l_1小
if (flag == 1)
{
l->tmp[i].readID = l_1[i_1].readID;
l->tmp[i].offset = l_1[i_1].offset;
l->tmp[i].self_offset = l_1[i_1].self_offset;
l->tmp[i].strand = l_1[i_1].strand;
i_1++;
i++;
}
else ///l_2小或者l_1 == l_2
{
l->tmp[i].readID = l_2[i_2].readID;
l->tmp[i].offset = l_2[i_2].offset;
l->tmp[i].self_offset = end_pos;
l->tmp[i].strand = strand;
i_2++;
i++;
}
}
while (i_1<len1)
{
l->tmp[i].readID = l_1[i_1].readID;
l->tmp[i].offset = l_1[i_1].offset;
l->tmp[i].self_offset = l_1[i_1].self_offset;
l->tmp[i].strand = l_1[i_1].strand;
i_1++;
i++;
}
while (i_2<len2)
{
l->tmp[i].readID = l_2[i_2].readID;
l->tmp[i].offset = l_2[i_2].offset;
l->tmp[i].self_offset = end_pos;
l->tmp[i].strand = strand;
i_2++;
i++;
}
k_mer_hit* k;
k = l->list;
l->list = l->tmp;
l->tmp = k;
l->length = l->length + n_lengh;
///debug_merge_Candidates_list(l, n_list, n_lengh, end_pos, i, i_1, i_2, len1, len2, strand);
}
/********************************for debug***************************************/
void debug_mode(uint64_t d, uint64_t thread_ID, uint64_t thread_num)
{
fprintf(stderr, "#%llu: Start debug_mode...\n", thread_ID);
uint64_t i;
for (i = thread_ID; i < 4,294,967,296; i = i + thread_num)
{
if(i%d != mod_d(0, i, d))
{
fprintf(stderr, "ERROR mode, i: %llu\n", i);
fprintf(stderr, "i mod d: %llu\n", i%d);
fprintf(stderr, "mod_d(0, i, d): %llu\n", mod_d(0, i, d));
}
}
fprintf(stderr, "#%llu: Finish debug_mode\n", thread_ID);
}
/********************************for debug***************************************/
void test_COUNT64()
{
uint64_t sb[7] = {5000000000, 6000000000, 7000000000, 8000000000, 9000000000, 10000000000 ,5000000000};
Count_Table* h;
///构建哈希表
init_Count_Table(&h);
int i;
khint_t k; ///这就是个迭代器
int absent;
for (i = 0; i < 7; i++)
{
///将5作为key插入到哈希表COUNT64中
///absent为0代表哈希表里面已经有这个key了
k = kh_put(COUNT64, h, sb[i], &absent);
///代表插入了一个哈希表中没有的元素
///则直接插入
if (absent)
{
kh_value(h, k) = i;
}
else ///哈希表中已有的元素
{
kh_value(h, k) = i;
}
}
for (i = 0; i < 7; i++)
{
///查询哈希表，key为k
k = kh_get(COUNT64, h, sb[i]);
if (k != kh_end(h))
{
fprintf(stderr, "value: %d\n", kh_value(h, k));
}
else
{
fprintf(stderr, "not found!\n");
}
}
kh_destroy(COUNT64, h);
}
int cmp_candidates_list(const void * a, const void * b)
{
long long r_pos_a, r_pos_b;
if((*((k_mer_hit*)a)).strand != (*((k_mer_hit*)b)).strand)
{
return (*((k_mer_hit*)a)).strand > (*((k_mer_hit*)b)).strand ? 1: -1;
}
else
{
if((*((k_mer_hit*)a)).readID != (*((k_mer_hit*)b)).readID)
{
return (*((k_mer_hit*)a)).readID > (*((k_mer_hit*)b)).readID ? 1: -1;
}
else
{
r_pos_a = (*((k_mer_hit*)a)).offset - (*((k_mer_hit*)a)).self_offset;
r_pos_b = (*((k_mer_hit*)b)).offset - (*((k_mer_hit*)b)).self_offset;
if(r_pos_a != r_pos_b)
{
return r_pos_a > r_pos_b ? 1: -1;
}
else
{
if((*((k_mer_hit*)a)).self_offset != (*((k_mer_hit*)b)).self_offset)
{
return (*((k_mer_hit*)a)).self_offset > (*((k_mer_hit*)b)).self_offset ? 1: -1;
}
else
{
return 0;
}
}
}
}
}
void sort_candidates(Candidates_list* candidates, long long readID,
overlap_region_alloc* overlap_list, All_reads* R_INF)
{
qsort(candidates->list, candidates->length, sizeof(k_mer_hit), cmp_candidates_list);
overlap_region tmp_region;
uint64_t i = 0;
long long current_pos_diff;
long long current_self_pos;
uint64_t current_ID;
uint64_t current_stand;
long long tmp_pos_distance;
long long tmp_self_pos_distance;
long long constant_distance = 5;
double error_rate = 0.05;
if (candidates->length == 0)
{
return;
}
// i = 0;
// for (i = 0; i < candidates->length; i++)
// {
// fprintf(stderr, "i: %d, ada_offset: %d, offset: %d, self_offset: %d, strand: %d\n",
// i, candidates->list[i].offset - candidates->list[i].self_offset,
// candidates->list[i].offset, candidates->list[i].self_offset,
// candidates->list[i].strand);
// }
i = 0;
while (i < candidates->length)
{
current_pos_diff = candidates->list[i].offset - candidates->list[i].self_offset;
current_self_pos = candidates->list[i].self_offset;
current_ID = candidates->list[i].readID;
current_stand = candidates->list[i].strand;
tmp_region.shared_seed = 1;
///这个是查询read的信息
tmp_region.x_id = readID;
tmp_region.x_pos_s = candidates->list[i].self_offset;
tmp_region.x_pos_e = candidates->list[i].self_offset;
tmp_region.x_pos_strand = 0; ///永远是0
///这个是被查询的read的信息
tmp_region.y_id = current_ID;
tmp_region.y_pos_s = candidates->list[i].offset;
tmp_region.y_pos_e = candidates->list[i].offset;
tmp_region.y_pos_strand = candidates->list[i].strand;
i++;
while (i < candidates->length)
{
if (current_ID == candidates->list[i].readID &&
current_stand == candidates->list[i].strand)
{
///这个一定是正值
tmp_pos_distance = candidates->list[i].offset - candidates->list[i].self_offset - current_pos_diff;
///这个不一定是正值
tmp_self_pos_distance = candidates->list[i].self_offset - current_self_pos;
if(tmp_self_pos_distance < 0)
{
///fprintf(stderr, "tmp_self_pos_distance: %d\n", tmp_self_pos_distance);
tmp_self_pos_distance = tmp_self_pos_distance * -1;
///fprintf(stderr, "tmp_self_pos_distance: %d\n", tmp_self_pos_distance);
}
///if (tmp_self_pos_distance >= 0)
{
tmp_self_pos_distance = tmp_self_pos_distance * error_rate + constant_distance;
if (tmp_pos_distance < tmp_self_pos_distance)
{
/****************************may have bugs********************************/
///i++;
// tmp_region.x_pos_e = candidates->list[i].self_offset;
// tmp_region.y_pos_e = candidates->list[i].offset;
/****************************may have bugs********************************/
tmp_region.shared_seed++;
if(candidates->list[i].self_offset < tmp_region.x_pos_s)
{
tmp_region.x_pos_s = candidates->list[i].self_offset;
}
if(candidates->list[i].self_offset > tmp_region.x_pos_e)
{
tmp_region.x_pos_e = candidates->list[i].self_offset;
}
if(candidates->list[i].offset < tmp_region.y_pos_s)
{
tmp_region.y_pos_s = candidates->list[i].offset;
}
if(candidates->list[i].offset > tmp_region.y_pos_e)
{
tmp_region.y_pos_e = candidates->list[i].offset;
}
/****************************may have bugs********************************/
i++;
/****************************may have bugs********************************/
continue;
}
}
}
break;
}
///自己和自己重叠的要排除
///if (tmp_region.x_id != tmp_region.y_id && tmp_region.shared_seed > 1)
if (tmp_region.x_id != tmp_region.y_id)
{
// fprintf(stderr, "i: %lld, candidates->length: %lld, tmp_region->shared_seed: %lld, x_pos_s: %lld, x_pos_e: %lld, y_pos_s: %lld, y_pos_e: %lld\n",
// i, candidates->length, tmp_region.shared_seed, tmp_region.x_pos_s, tmp_region.x_pos_e, tmp_region.y_pos_s, tmp_region.y_pos_e);
// fprintf(stderr, "\n");
// fprintf(stderr, "shared_seed: %d, x_pos_s: %d, x_pos_e: %d, y_pos_s: %d, y_pos_e: %d\n",
// tmp_region.shared_seed, tmp_region.x_pos_s, tmp_region.x_pos_e, tmp_region.y_pos_s, tmp_region.y_pos_e);
///append_overlap_region_alloc(overlap_list, &tmp_region, R_INF);
append_overlap_region_alloc_from_existing(overlap_list, &tmp_region, R_INF);
}
}
///以x_pos_e，即结束位置为主元排序
///qsort(overlap_list->list, overlap_list->length, sizeof(overlap_region), cmp_by_x_pos_e);
///qsort(overlap_list->list, overlap_list->length, sizeof(overlap_region), cmp_by_x_pos_s);
clear_Candidates_list(candidates);
}
void init_fake_cigar(Fake_Cigar* x)
{
x->buffer = NULL;
x->length = 0;
x->size = 0;
}
void destory_fake_cigar(Fake_Cigar* x)
{
if(x->size > 0)
{
free(x->buffer);
}
}
void clear_fake_cigar(Fake_Cigar* x)
{
x->length = 0;
}
void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift)
{
if(x->length + 1 > x->size)
{
x->size = (x->length + 1) * 2;
x->buffer = (uint64_t*)realloc(x->buffer, sizeof(uint64_t) * x->size);
}
x->buffer[x->length] = gap_site;
x->buffer[x->length] = x->buffer[x->length] << 32;
if(gap_shift < 0)
{
gap_shift = gap_shift * -1;
gap_site = gap_shift;
gap_site = gap_site << 1;
gap_site = gap_site | ((uint32_t)1);
}
else
{
gap_site = gap_shift;
gap_site = gap_site << 1;
}
x->buffer[x->length] = x->buffer[x->length] | ((uint32_t)gap_site);
x->length++;
}
void resize_fake_cigar(Fake_Cigar* x, long long size)
{
if(size > x->size)
{
x->size = size;
x->buffer = (uint64_t*)realloc(x->buffer, sizeof(uint64_t) * x->size);
}
x->length = 0;
}
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