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chhylp123
2021-05-30 09:02:25 -04:00
parent a39f01f4d8
commit e774a83be2
18 changed files with 2497 additions and 207 deletions
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Hash_Table.cpp
+164 -1
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@@ -193,6 +193,168 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
if(add_beg_end == 1)
{
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;
/****************************may have bugs********************************/
///long long pre_distance_gap = init_distance_gap;
long long pre_distance_gap = 0xfffffffffffffff;
/****************************may have bugs********************************/
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(add_beg_end == 1 && get_fake_gap_pos(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1) != (long long)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));
}
}
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;
}
int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp,
ma_utg_v *ua, int add_beg_end)
{
if (list->length + 1 > list->size)
{
list->size = list->size * 2;
list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
/// need to set new space to be 0
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 = ua->a[tmp->x_id].len - tmp->x_pos_e - 1;
long long y_right_length = ua->a[tmp->y_id].len - tmp->y_pos_e - 1;
if(x_right_length <= y_right_length)
{
tmp->x_pos_e = ua->a[tmp->x_id].len - 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 = ua->a[tmp->y_id].len - 1;
}
if (tmp->x_pos_strand == 1)
{
list->list[list->length].x_id = tmp->x_id;
list->list[list->length].x_pos_e = ua->a[tmp->x_id].len - tmp->x_pos_s - 1;
list->list[list->length].x_pos_s = ua->a[tmp->x_id].len - 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 = ua->a[tmp->y_id].len - tmp->y_pos_s - 1;
list->list[list->length].y_pos_s = ua->a[tmp->y_id].len - 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));
if(add_beg_end == 1)
{
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
}
long long distance_gap;
/****************************may have bugs********************************/
///long long pre_distance_gap = 0;
long long pre_distance_gap = 0xfffffffffffffff;
/****************************may have bugs********************************/
long long i = 0;
for (i = 0; i < (long long)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),
ua->a[tmp->x_id].len - get_fake_gap_pos(&(tmp->f_cigar), i) - 1,
pre_distance_gap);
}
}
if(add_beg_end == 1 && get_fake_gap_pos(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1) != (long long)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));
if(add_beg_end == 1)
{
@@ -422,7 +584,7 @@ int32_t ha_chain_check(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min_sc
}
///double band_width_threshold = 0.05;
void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result,
long long 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;
@@ -613,6 +775,7 @@ skip_dp:
i = dp->pre[i];
}
}
return chainLen;
}
void calculate_overlap_region_by_chaining_back(Candidates_list* candidates, overlap_region_alloc* overlap_list,