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r238: got rid of LIS chaining

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Heng Li
2020-04-13 14:44:10 -04:00
parent b333addb6c
commit 946a0f4115
2 changed files with 14 additions and 41 deletions
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CommandLines.h
+1 -1
View File
@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r237"
#define HA_VERSION "0.3.0-dirty-r238"
#define VERBOSE 0
Hash_Table.cpp
+13 -40
View File
@@ -337,48 +337,22 @@ long long get_chainLen(long long x_beg, long long x_end, long long xLen,
return x_end - x_beg + 1;
}
static int32_t ha_kmer_hit_lis(int32_t n, const k_mer_hit *a, int32_t *b, int32_t *M)
int32_t ha_chain_check(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min_sc, double bw_thres)
{
int32_t i, k, L = 0, *P = b;
for (i = 0; i < n; ++i) {
int32_t lo = 1, hi = L, newL;
while (lo <= hi) {
int32_t mid = (lo + hi + 1) >> 1;
if (a[M[mid]].self_offset < a[i].self_offset) lo = mid + 1;
else hi = mid - 1;
}
newL = lo, P[i] = M[newL - 1], M[newL] = i;
if (newL > L) L = newL;
}
k = M[L];
memcpy(M, P, n * sizeof(int32_t));
for (i = L - 1; i >= 0; --i) b[i] = k, k = M[k];
return L;
}
int32_t ha_chain_lis_core(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min_sc, double bw_thres)
{
int32_t *tmp = (int32_t*)dp->tmp;
int32_t i, m, *b = tmp, *M = tmp + n_a;
int32_t tot_indel = 0, tot_len = 0;
int32_t i, tot_indel = 0, tot_len = 0;
double bw_pen;
if (n_a < 2) return -1;
if (n_a == 0) return -1;
for (i = 1; i < n_a; ++i)
if (a[i-1].self_offset >= a[i].self_offset)
break;
if (i == n_a) {
for (i = 0; i < n_a; ++i)
b[i] = i;
m = n_a;
} else m = ha_kmer_hit_lis(n_a, a, b, M);
if (m < n_a>>1) return -1;
if (i < n_a) return -1;
bw_pen = 1.0 / bw_thres;
dp->score[0] = a[b[0]].good? min_sc : min_sc>>1;
dp->score[0] = a[0].good? min_sc : min_sc>>1;
dp->pre[0] = -1, dp->indels[0] = 0, dp->self_length[0] = 0;
for (i = 1; i < m; ++i) {
int32_t j0 = b[i-1], j1 = b[i], score, dg;
int32_t dx = (int32_t)a[j1].offset - (int32_t)a[j0].offset;
int32_t dy = (int32_t)a[j1].self_offset - (int32_t)a[j0].self_offset;
for (i = 1; i < n_a; ++i) {
int32_t score, dg;
int32_t dx = (int32_t)a[i].offset - (int32_t)a[i-1].offset;
int32_t dy = (int32_t)a[i].self_offset - (int32_t)a[i-1].self_offset;
int32_t dd = dx > dy? dx - dy : dy - dx;
double gap_rate;
tot_indel += dd;
@@ -387,7 +361,7 @@ int32_t ha_chain_lis_core(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min
dg = dx < dy? dx : dy;
if (dd > THRESHOLD_MAX_SIZE && dd > dg * bw_thres) break;
score = dg < min_sc? dg : min_sc;
if (!a[j1].good) score >>= 1;
if (!a[i].good) score >>= 1;
gap_rate = (double)tot_indel / tot_len;
score -= (int)(gap_rate * score * bw_pen);
dp->score[i] = dp->score[i-1] + score;
@@ -395,9 +369,8 @@ int32_t ha_chain_lis_core(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min
dp->indels[i] = tot_indel;
dp->self_length[i] = tot_len;
}
if (i < m) return -1;
for (i = 0; i < m; ++i) a[i] = a[b[i]];
return m;
if (i < n_a) return -1;
return n_a;
}
///double band_width_threshold = 0.05;
@@ -417,7 +390,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
resize_Chain_Data(dp, a_n);
ret = ha_chain_lis_core(a, a_n, dp, min_score, band_width_threshold);
ret = ha_chain_check(a, a_n, dp, min_score, band_width_threshold);
if (ret > 0) {
a_n = ret;
goto skip_dp;