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use updated kalloc macros (#1051) 

* use updated kalloc macros

* review

* get the reference

* store the reference

* last one
This commit is contained in:
Chris Seymour 2023-04-21 15:45:53 +01:00 committed by GitHub
parent c3d461e22a
commit e68d868806
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3 changed files with 16 additions and 16 deletions
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4
kalloc.h
View File

@ -37,7 +37,7 @@ void km_stat_print(const void *km);
#define KEXPAND(km, a, m) do { \
(m) = (m) >= 4? (m) + ((m)>>1) : 16; \
KREALLOC((km), (a), (m)); \
a = krealloc((km), (a), (m) * sizeof(a)) ; \
} while (0)
#ifndef klib_unused
@ -56,7 +56,7 @@ void km_stat_print(const void *km);
} kmp_##name##_t; \
SCOPE kmp_##name##_t *kmp_init_##name(void *km) { \
kmp_##name##_t *mp; \
KCALLOC(km, mp, 1); \
mp = Kcalloc(km, kmp_##name##_t, 1); \
mp->km = km; \
return mp; \
} \

26
lchain.c
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@ -35,7 +35,7 @@ uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_
for (i = 0, n_z = 0; i < n; ++i) // precompute n_z
if (f[i] >= min_sc) ++n_z;
if (n_z == 0) return 0;
KMALLOC(km, z, n_z);
z = Kmalloc(km, mm128_t, n_z);
for (i = 0, k = 0; i < n; ++i) // populate z[]
if (f[i] >= min_sc) z[k].x = f[i], z[k++].y = i;
radix_sort_128x(z, z + n_z);
@ -54,7 +54,7 @@ uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_
else n_v = n_v0;
}
}
KMALLOC(km, u, n_u);
u = Kmalloc(km, uint64_t, n_u);
memset(t, 0, n * 4);
for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // populate u[]
if (t[z[k].y] == 0) {
@ -82,7 +82,7 @@ static mm128_t *compact_a(void *km, int32_t n_u, uint64_t *u, int32_t n_v, int32
int64_t i, j, k;
// write the result to b[]
KMALLOC(km, b, n_v);
b = Kmalloc(km, mm128_t, n_v);
for (i = 0, k = 0; i < n_u; ++i) {
int32_t k0 = k, ni = (int32_t)u[i];
for (j = 0; j < ni; ++j)
@ -91,13 +91,13 @@ static mm128_t *compact_a(void *km, int32_t n_u, uint64_t *u, int32_t n_v, int32
kfree(km, v);
// sort u[] and a[] by the target position, such that adjacent chains may be joined
KMALLOC(km, w, n_u);
w = Kmalloc(km, mm128_t, n_u);
for (i = k = 0; i < n_u; ++i) {
w[i].x = b[k].x, w[i].y = (uint64_t)k<<32|i;
k += (int32_t)u[i];
}
radix_sort_128x(w, w + n_u);
KMALLOC(km, u2, n_u);
u2 = Kmalloc(km, uint64_t, n_u);
for (i = k = 0; i < n_u; ++i) {
int32_t j = (int32_t)w[i].y, n = (int32_t)u[j];
u2[i] = u[j];
@ -160,10 +160,10 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
if (max_dist_x < bw) max_dist_x = bw;
if (max_dist_y < bw && !is_cdna) max_dist_y = bw;
if (is_cdna) max_drop = INT32_MAX;
KMALLOC(km, p, n);
KMALLOC(km, f, n);
KMALLOC(km, v, n);
KCALLOC(km, t, n);
p = Kmalloc(km, int64_t, n);
f = Kmalloc(km, int32_t, n);
v = Kmalloc(km, int32_t, n);
t = Kcalloc(km, int32_t, n);
// fill the score and backtrack arrays
for (i = 0, max_ii = -1; i < n; ++i) {
@ -264,10 +264,10 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
}
if (max_dist < bw) max_dist = bw;
if (max_dist_inner <= 0 || max_dist_inner >= max_dist) max_dist_inner = 0;
KMALLOC(km, p, n);
KMALLOC(km, f, n);
KCALLOC(km, t, n);
KMALLOC(km, v, n);
p = Kmalloc(km, int64_t, n);
f = Kmalloc(km, int32_t, n);
t = Kcalloc(km, int32_t, n);
v = Kmalloc(km, int32_t, n);
mem_mp = km_init2(km, 0x10000);
mp = kmp_init_rmq(mem_mp);

2
seed.c
View File

@ -7,7 +7,7 @@ void mm_seed_mz_flt(void *km, mm128_v *mv, int32_t q_occ_max, float q_occ_frac)
mm128_t *a;
size_t i, j, st;
if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return;
KMALLOC(km, a, mv->n);
a = Kmalloc(km, mm128_t, mv->n);
for (i = 0; i < mv->n; ++i)
a[i].x = mv->a[i].x, a[i].y = i;
radix_sort_128x(a, a + mv->n);