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r177: combine the hifiasm and minimap2 heuristics

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Heng Li
2020-04-01 23:07:42 -04:00
parent b7e5d1c4d3
commit 878fe943c3
2 changed files with 13 additions and 7 deletions
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18
Hash_Table.cpp
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@@ -405,7 +405,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
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;
long long self_pos, pos, max_j, max_i, max_score, score;
long long distance_pos, distance_self_pos, distance_gap, distance_min;
///double band_width_threshold = 0.05;
double band_width_penalty = 1 / band_width_threshold;
@@ -419,14 +419,15 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
for (i = 0; i < a_n; ++i) dp->tmp[i] = -1;
for (i = 0; i < a_n; ++i)
{
int n_chn_skip = 0;
int n_max_skip = 0;
pos = a[i].offset;
self_pos = a[i].self_offset;
max_j = -1;
max_score = min_score;
n_skip = 0;
max_indels = 0;
max_self_length = 0;
///may have a pre-cut condition for j
for (j = i - 1; j >= 0; --j)
@@ -466,10 +467,15 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
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)
n_max_skip = 0;
if (n_chn_skip > 0) --n_chn_skip;
} else {
if (++n_max_skip > max_skip)
break;
if (dp->tmp[j] == i) {
if (++n_chn_skip > max_skip)
break;
}
}
if (dp->pre[j] >= 0) dp->tmp[dp->pre[j]] = i;
}