r1116: cut long chains at weak points
This commit is contained in:
Heng Li
parent
db37fc43a7
commit
fcaadc22b7
33
lchain.c
33
lchain.c
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@ -6,23 +6,25 @@
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#include "kalloc.h"
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#include "krmq.h"
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static int64_t mg_chain_bk_end(const mm128_t *z, const int32_t *f, const int64_t *p, int32_t *t, int64_t k)
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static int64_t mg_chain_bk_end(int32_t max_drop, const mm128_t *z, const int32_t *f, const int64_t *p, int32_t *t, int64_t k)
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{
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int64_t i = z[k].y, end_i = -1;
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int64_t i = z[k].y, end_i = -1, max_i = i;
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int32_t max_s = 0;
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if (i < 0 || t[i] != 0) return i;
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while (1) {
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do {
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int32_t s;
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t[i] = 2;
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end_i = i = p[i];
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s = i < 0? z[k].y : (int32_t)z[k].x - f[i];
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if (i < 0 || t[i] != 0) break;
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}
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if (s > max_s) max_s = s, max_i = i;
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else if (max_s - s > max_drop) break;
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} while (i >= 0 && t[i] == 0);
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for (i = z[k].y; i >= 0 && i != end_i; i = p[i]) // reset modified t[]
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t[i] = 0;
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return end_i;
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return max_i;
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}
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uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_t *p, int32_t *v, int32_t *t, int32_t min_cnt, int32_t min_sc, int32_t *n_u_, int32_t *n_v_)
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uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_t *p, int32_t *v, int32_t *t, int32_t min_cnt, int32_t min_sc, int32_t max_drop, int32_t *n_u_, int32_t *n_v_)
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{
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mm128_t *z;
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uint64_t *u;
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@ -40,10 +42,10 @@ uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_
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memset(t, 0, n * 4);
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for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // precompute n_u
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if (t[z[k].y] != 0) {
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if (t[z[k].y] == 0) {
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int64_t n_v0 = n_v, end_i;
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int32_t sc;
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end_i = mg_chain_bk_end(z, f, p, t, k);
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end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
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for (i = z[k].y; i != end_i; i = p[i])
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++n_v, t[i] = 1;
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sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
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@ -55,10 +57,10 @@ uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_
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KMALLOC(km, u, n_u);
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memset(t, 0, n * 4);
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for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // populate u[]
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if (t[z[k].y] != 0) {
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if (t[z[k].y] == 0) {
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int64_t n_v0 = n_v, end_i;
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int32_t sc;
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end_i = mg_chain_bk_end(z, f, p, t, k);
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end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
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for (i = z[k].y; i != end_i; i = p[i])
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v[n_v++] = i, t[i] = 1;
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sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
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@ -146,7 +148,7 @@ static inline int32_t comput_sc(const mm128_t *ai, const mm128_t *aj, int32_t ma
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mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
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int is_cdna, int n_seg, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
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{ // TODO: make sure this works when n has more than 32 bits
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int32_t *f, *t, *v, n_u, n_v, mmax_f = 0;
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int32_t *f, *t, *v, n_u, n_v, mmax_f = 0, max_drop = bw;
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int64_t *p, i, j, max_ii, st = 0, n_iter = 0;
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uint64_t *u;
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@ -157,6 +159,7 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
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}
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if (max_dist_x < bw) max_dist_x = bw;
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if (max_dist_y < bw && !is_cdna) max_dist_y = bw;
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if (is_cdna) max_drop = INT32_MAX;
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KMALLOC(km, p, n);
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KMALLOC(km, f, n);
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KMALLOC(km, v, n);
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@ -203,7 +206,7 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
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if (mmax_f < max_f) mmax_f = max_f;
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}
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u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, &n_u, &n_v);
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u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
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*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
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kfree(km, p); kfree(km, f); kfree(km, t);
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if (n_u == 0) {
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@ -247,7 +250,7 @@ static inline int32_t comput_sc_simple(const mm128_t *ai, const mm128_t *aj, flo
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mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_skip, int cap_rmq_size, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
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int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
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{
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int32_t *f,*t, *v, n_u, n_v, mmax_f = 0, max_rmq_size = 0;
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int32_t *f,*t, *v, n_u, n_v, mmax_f = 0, max_rmq_size = 0, max_drop = bw;
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int64_t *p, i, i0, st = 0, st_inner = 0, n_iter = 0;
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uint64_t *u;
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lc_elem_t *root = 0, *root_inner = 0;
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@ -355,7 +358,7 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
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}
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km_destroy(mem_mp);
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u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, &n_u, &n_v);
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u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
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*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
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kfree(km, p); kfree(km, f); kfree(km, t);
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if (n_u == 0) {
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