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Merge overlap

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This commit is contained in:
Haoyu Cheng
2019-05-18 01:03:24 -04:00
parent 87a6091ffe
commit ddd96d8456
11 changed files with 619 additions and 21 deletions
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413
Hash_Table.cpp
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@@ -4,6 +4,39 @@
#include "Hash_Table.h"
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);
}
void destory_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
free(list->list);
}
void clear_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
list->length = 0;
}
void append_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list, k_mer_pos* n_list, uint64_t n_length)
{
list->length++;
if (list->length > 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 - 1].list = n_list;
list->list[list->length - 1].length = n_length;
}
void init_Count_Table(Count_Table** table)
{
*table = kh_init(COUNT64);
@@ -300,6 +333,386 @@ int cmp_k_mer_pos(const void * a, const void * b)
}
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;
}
void clear_Candidates_list(Candidates_list* l)
{
l->length = 0;
l->foward_pos = 0;
l->rc_pos = 0;
}
void destory_Candidates_list(Candidates_list* l)
{
free(l->list);
free(l->tmp);
}
///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);
}