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reverted to the older k_mer_hit definition

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Heng Li
2020-03-27 10:40:31 -04:00
parent 10ed8b36ec
commit 7271c106e4
4 changed files with 40 additions and 48 deletions
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Hash_Table.cpp
+18 -20
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@@ -347,7 +347,7 @@ void debug_chain(k_mer_hit* a, long long a_n, Chain_Data* dp)
if(j != -1)
{
distance_self_pos = a[current_j].self_offset - a[j].self_offset;
distance_pos = ha_hit_get_offset(&a[current_j]) - ha_hit_get_offset(&a[j]);
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;
@@ -421,7 +421,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
// fill the score and backtrack arrays
for (i = 0; i < a_n; ++i)
{
pos = ha_hit_get_offset(&a[i]);
pos = a[i].offset;
self_pos = a[i].self_offset;
max_j = -1;
max_score = min_score;
@@ -433,7 +433,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
///may have a pre-cut condition for j
for (j = i - 1; j >= 0; --j)
{
distance_pos = pos - ha_hit_get_offset(&a[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
@@ -502,12 +502,12 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
max_score = dp->score[i];
max_i = i;
mini_xLen = get_chainLen(a[i].self_offset, a[i].self_offset, x_readLen,
ha_hit_get_offset(&a[i]), ha_hit_get_offset(&a[i]), y_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,
ha_hit_get_offset(&a[i]), ha_hit_get_offset(&a[i]), y_readLen);
a[i].offset, a[i].offset, y_readLen);
if(tmp_xLen < mini_xLen)
{
@@ -524,12 +524,12 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
///not a has been sorted by offset, that means has been sorted by query offset
i = max_i;
result->x_pos_e = a[i].self_offset;
result->y_pos_e = ha_hit_get_offset(&a[i]);
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 - ha_hit_get_offset(&a[i]);
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
@@ -541,7 +541,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
while (i >= 0)
{
distance_self_pos = result->x_pos_e - a[i].self_offset;
distance_pos = result->y_pos_e - ha_hit_get_offset(&a[i]);
distance_pos = result->y_pos_e - a[i].offset;
distance_gap = distance_pos - distance_self_pos;
if(distance_gap != pre_distance_gap)
{
@@ -552,7 +552,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
chainLen++;
result->x_pos_s = a[i].self_offset;
result->y_pos_s = ha_hit_get_offset(&a[i]);
result->y_pos_s = a[i].offset;
i = dp->pre[i];
}
}
@@ -562,7 +562,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
while (i >= 0)
{
distance_self_pos = result->x_pos_e - a[i].self_offset;
distance_pos = result->y_pos_e - ha_hit_get_offset(&a[i]);
distance_pos = result->y_pos_e - a[i].offset;
distance_gap = distance_pos - distance_self_pos;
if(distance_gap == pre_distance_gap)
{
@@ -577,7 +577,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
chainLen++;
result->x_pos_s = a[i].self_offset;
result->y_pos_s = ha_hit_get_offset(&a[i]);
result->y_pos_s = a[i].offset;
i = dp->pre[i];
}
}
@@ -604,8 +604,8 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
i = 0;
while (i < candidates->length)
{
current_ID = ha_hit_get_readID(&candidates->list[i]);
current_stand = ha_hit_get_rev(&candidates->list[i]);
current_ID = candidates->list[i].readID;
current_stand = candidates->list[i].strand;
///reference read
tmp_region.x_id = readID;
@@ -623,9 +623,9 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
while (i < candidates->length
&&
current_ID == ha_hit_get_readID(&candidates->list[i])
current_ID == candidates->list[i].readID
&&
current_stand == ha_hit_get_rev(&candidates->list[i]))
current_stand == candidates->list[i].strand)
{
sub_region_end = i;
i++;
@@ -733,13 +733,13 @@ void test_single_list(Candidates_list* candidates, k_mer_pos* n_list, uint64_t n
for (; j < candidates->length; j++)
{
if (
n_list[i].offset == (uint64_t)ha_hit_get_offset(&candidates->list[j])
n_list[i].offset == (uint64_t)candidates->list[j].offset
&&
n_list[i].readID == ha_hit_get_readID(&candidates->list[j])
n_list[i].readID == candidates->list[j].readID
&&
end_pos == (uint64_t)candidates->list[j].self_offset
&&
strand == ha_hit_get_rev(&candidates->list[j])
strand == candidates->list[j].strand
)
{
break;
@@ -794,7 +794,6 @@ void init_Candidates_list(Candidates_list* l)
l->length = 0;
l->size = 0;
l->list = NULL;
l->tmp = NULL;
init_Chain_Data(&(l->chainDP));
}
@@ -807,7 +806,6 @@ void clear_Candidates_list(Candidates_list* l)
void destory_Candidates_list(Candidates_list* l)
{
free(l->list);
free(l->tmp);
destory_Chain_Data(&(l->chainDP));
}