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r176: enabled the minimap2 chaining heuristic

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This commit is contained in:
Heng Li
2020-04-01 22:06:14 -04:00
parent e75b93ae12
commit b7e5d1c4d3
5 changed files with 44 additions and 65 deletions
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Hash_Table.cpp
+29 -45
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@@ -356,14 +356,12 @@ void debug_chain(k_mer_hit* a, long long a_n, Chain_Data* dp)
if(indels != dp->indels[i])
{
fprintf(stderr, "indels: %lld, dp->indels[i]: %lld\n",
indels, dp->indels[i]);
fprintf(stderr, "indels: %lld, dp->indels[i]: %ld\n", indels, (long)dp->indels[i]);
}
if(selfLen != dp->self_length[i])
{
fprintf(stderr, "selfLen: %lld, dp->self_length[i]: %lld\n",
selfLen, dp->self_length[i]);
fprintf(stderr, "selfLen: %lld, dp->self_length[i]: %ld\n", selfLen, (long)dp->self_length[i]);
}
}
@@ -418,6 +416,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
resize_Chain_Data(dp, a_n);
// fill the score and backtrack arrays
for (i = 0; i < a_n; ++i) dp->tmp[i] = -1;
for (i = 0; i < a_n; ++i)
{
pos = a[i].offset;
@@ -461,26 +460,18 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
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********************************/
///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) --n_skip;
} else if (dp->tmp[j] == i) {
if (++n_skip > max_skip)
break;
}
if (dp->pre[j] >= 0) dp->tmp[dp->pre[j]] = i;
}
dp->score[i] = max_score;
@@ -636,14 +627,10 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
}
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));
chain_DP(candidates->list + sub_region_beg,
sub_region_end - sub_region_beg + 1, &(candidates->chainDP), &tmp_region, band_width_threshold,
25, Get_READ_LENGTH((*R_INF), tmp_region.x_id), Get_READ_LENGTH((*R_INF), tmp_region.y_id));
// chain_DP_back(candidates->list + sub_region_beg,
// sub_region_end - sub_region_beg + 1, &(candidates->chainDP), &tmp_region, band_width_threshold);
///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)
{
@@ -720,12 +707,7 @@ void test_single_list(Candidates_list* candidates, k_mer_pos* n_list, uint64_t n
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;
memset(x, 0, sizeof(Chain_Data));
}
void clear_Chain_Data(Chain_Data* x)
@@ -739,18 +721,20 @@ void destory_Chain_Data(Chain_Data* x)
free(x->pre);
free(x->indels);
free(x->self_length);
free(x->tmp);
}
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));
}
if (size > x->size) {
x->size = size;
kroundup64(x->size);
REALLOC(x->score, x->size);
REALLOC(x->pre, x->size);
REALLOC(x->indels, x->size);
REALLOC(x->self_length, x->size);
REALLOC(x->tmp, x->size);
}
}
void init_Candidates_list(Candidates_list* l)