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r328: use binomial heap for general cases

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Heng Li
2020-11-01 22:49:06 -05:00
parent 6fa4d44426
commit dcb583bd69
3 changed files with 49 additions and 24 deletions
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52
sketch.cpp
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@@ -4,6 +4,10 @@
#include <string.h>
#include "kvec.h"
#include "htab.h"
#include "ksort.h"
#define MAX_HIGH_OCC 3 // TODO: don't hard code if we need to tune this parameter
#define MAX_MAX_HIGH_OCC 16
typedef struct { // a simplified version of kdq
int front, count;
@@ -30,11 +34,18 @@ static inline int mzcmp(const ha_mz1_t *a, const ha_mz1_t *b)
return a->rid < b->rid? -1 : a->rid > b->rid? 1 : ((a->x > b->x) - (a->x < b->x));
}
static void select_mz(ha_mz1_v *p, int len)
{
static const ha_mz1_t dummy = { UINT64_MAX, (1<<28) - 1, 0, 0 };
#define mz_lt(a, b) (mzcmp(&(a), &(b)) < 0)
KSORT_INIT(mz, ha_mz1_t, mz_lt)
static void select_mz(ha_mz1_v *p, int len, int max_high_occ)
{ // for high-occ minimizers, choose up to max_high_occ in each high-occ streak
int32_t i, last0 = -1, n = (int32_t)p->n, m = 0;
ha_mz1_t b[MAX_MAX_HIGH_OCC]; // this is to avoid a heap allocation
if (n == 0 || n == 1) return;
assert(n < 1<<27); // 27 is the number of bits for ha_mz1_t::pos; this should be safe as there are more bases than minimizers
if (max_high_occ > MAX_MAX_HIGH_OCC)
max_high_occ = MAX_MAX_HIGH_OCC;
for (i = 0; i < n; ++i)
if (p->a[i].rid != 0) ++m;
if (m == 0) return; // no high-frequency k-mers; do nothing
@@ -43,25 +54,22 @@ static void select_mz(ha_mz1_v *p, int len)
if (i - last0 > 1) {
int32_t ps = last0 < 0? 0 : p->a[last0].pos;
int32_t pe = i == n? len : p->a[i].pos;
int32_t j, st = last0 + 1, en = i;
ha_mz1_t min1 = dummy, min2 = dummy, min3 = dummy;
int32_t min1_i = -1, min2_i = -1, min3_i = -1;
for (j = st; j < en; ++j) { // choose up to three minimum k-mers
if (mzcmp(&p->a[j], &min1) < 0)
min3 = min2, min3_i = min2_i, min2 = min1, min2_i = min1_i, min1 = p->a[j], min1_i = j;
else if (mzcmp(&p->a[j], &min2) < 0)
min3 = min2, min3_i = min2_i, min2 = p->a[j], min2_i = j;
else if (mzcmp(&p->a[j], &min3) < 0)
min3 = p->a[j], min3_i = j;
}
if (min1_i >= 0 && p->a[min1_i].rid < pe - ps) {
p->a[min1_i].rid = 0;
if (min2_i >= 0 && p->a[min2_i].rid < pe - ps) {
p->a[min2_i].rid = 0;
if (min3_i >= 0 && p->a[min3_i].rid < pe - ps)
p->a[min3_i].rid = 0;
int32_t j, k, st = last0 + 1, en = i;
for (j = st, k = 0; j < en && k < max_high_occ; ++j, ++k)
b[k] = p->a[j], b[k].pos = j; // b[].pos keeps the index in p->a[]
if (j < en) { // if there are more, choose top max_high_occ
assert(k == max_high_occ);
ks_heapmake_mz(max_high_occ, b); // initialize the binomial heap
for (; j < en; ++j) {
if (mz_lt(p->a[j], b[0])) { // then update the heap
b[0] = p->a[j], b[0].pos = j;
ks_heapdown_mz(0, max_high_occ, b);
}
}
}
for (j = 0; j < k; ++j)
if (b[j].rid < pe - ps)
p->a[b[j].pos].rid = 0;
}
last0 = i;
}
@@ -149,7 +157,7 @@ void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc,
cnt = hf? ha_ft_cnt(hf, y) : 0;
filtered = (cnt >= 1<<28);
if (dbg_ct != NULL) kv_push(uint64_t, dbg_ct->a, ((((uint64_t)(query_ct_index(ha_ct_table, y))<<1)|filtered)<<32)|(uint64_t)(i));
if (!filtered) info.x = y, info.rid = cnt, info.pos = i, info.rev = z, info.span = kmer_span;
if (!filtered) info.x = y, info.rid = cnt, info.pos = i, info.rev = z, info.span = kmer_span; // initially ha_mz1_t::rid keeps the k-mer count
if (k_flag != NULL) k_flag->a.a[i]++;
if (k_flag != NULL && filtered > 0) k_flag->a.a[i]++;
}
@@ -197,7 +205,7 @@ void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc,
}
if (min.x != UINT64_MAX)
kv_push(ha_mz1_t, *p, min);
select_mz(p, len);
select_mz(p, len, MAX_HIGH_OCC);
for (i = 0; i < (int)p->n; ++i) // populate .rid as this was keeping counts
p->a[i].rid = rid;
}