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fix bugs for overlaps of different length

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This commit is contained in:
Haoyu Cheng
2019-12-09 17:07:11 -05:00
parent fca9c8db15
commit 09603432e5
11 changed files with 1726 additions and 94 deletions
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Hash_Table.cpp
+142 -16
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@@ -643,11 +643,13 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
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->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)
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;
}
@@ -1244,10 +1246,41 @@ void debug_chain(k_mer_hit* a, long long a_n, Chain_Data* dp)
}
}
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)
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;
@@ -1294,31 +1327,36 @@ double band_width_threshold)
continue;
}
///min distance
distance_min = distance_pos < distance_self_pos? distance_pos:distance_self_pos;
score = distance_min < min_score? distance_min : min_score;
/**
log_distance_gap = distance_gap? ilog2_32(distance_gap) : 0;
score -= (long long)(distance_gap * 0.01 * min_score) + (log_distance_gap/2);
**/
gap_rate = (double)((double)(total_indels)/(double)(total_self_length));
///if the gap rate > 0.05, score will be negative
///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;
if (n_skip > 0)
/****************************may have bugs********************************/
n_skip = 0;
/****************************may have bugs********************************/
}/****************************may have bugs********************************/
else
{
n_skip++;
if(n_skip > max_skip)
{
n_skip--;
break;
}
}
/****************************may have bugs********************************/
}
dp->score[i] = max_score;
@@ -1331,16 +1369,34 @@ double band_width_threshold)
///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;
}
}
}
@@ -1350,6 +1406,7 @@ double band_width_threshold)
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;
@@ -1515,7 +1572,6 @@ uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_thresh
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)
@@ -1562,9 +1618,80 @@ uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_thresh
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);
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)
@@ -2467,7 +2594,6 @@ int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
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));