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r330: unimap heuristic for mz sampling

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Heng Li
2021-01-21 11:05:37 -05:00
parent 02f0b5dd22
commit da672118e5
6 changed files with 14 additions and 12 deletions
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sketch.cpp
+8 -8
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@@ -6,7 +6,7 @@
#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_HIGH_OCC 8 // 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
@@ -37,15 +37,13 @@ static inline int mzcmp(const ha_mz1_t *a, const ha_mz1_t *b)
#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)
static void select_mz(ha_mz1_v *p, int len, int sample_dist)
{ // 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
@@ -55,6 +53,9 @@ static void select_mz(ha_mz1_v *p, int len, int max_high_occ)
int32_t ps = last0 < 0? 0 : p->a[last0].pos;
int32_t pe = i == n? len : p->a[i].pos;
int32_t j, k, st = last0 + 1, en = i;
int32_t max_high_occ = (int32_t)((double)(pe - ps) / sample_dist + .499);
if (max_high_occ > MAX_MAX_HIGH_OCC)
max_high_occ = MAX_MAX_HIGH_OCC;
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[]
ks_heapmake_mz(k, b); // initialize the binomial heap
@@ -66,8 +67,7 @@ static void select_mz(ha_mz1_v *p, int len, int max_high_occ)
}
//ks_heapsort_mz(k, b); // sorting is not needed for now
for (j = 0; j < k; ++j)
if (b[j].rid < pe - ps)
p->a[b[j].pos].rid = 0;
p->a[b[j].pos].rid = 0;
}
last0 = i;
}
@@ -89,7 +89,7 @@ static void select_mz(ha_mz1_v *p, int len, int max_high_occ)
* @param is_hpc homopolymer-compressed or not
* @param p minimizers
*/
void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct)
void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf, int sample_dist, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct)
{ ///in default, w = 51, k = 51, is_hpc = 1
/**
uint64_t x;
@@ -202,7 +202,7 @@ 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, MAX_HIGH_OCC);
if (sample_dist > w) 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;
}