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mm2-fast-v2.22 init

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Saurabh
2021-11-27 10:42:22 -05:00
committed by Heng Li
parent c7cdb758db
commit ba2f19ba37
12 changed files with 3535 additions and 20 deletions
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seed.c
+45
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@@ -1,9 +1,40 @@
#include "mmpriv.h"
#include "kalloc.h"
#include "ksort.h"
#include <stdlib.h>
#include<algorithm>
#include <x86intrin.h>
#ifdef LISA_HASH
#include "lisa_hash.h"
extern lisa_hash<uint64_t, uint64_t> *lh;
#endif
extern uint64_t minimizer_lookup_time;
mm_seed_t *mm_seed_collect_all(void *km, const mm_idx_t *mi, const mm128_v *mv, int32_t *n_m_)
{
#ifdef MANUAL_PROFILING
uint64_t lookup_start = __rdtsc();
#endif
#ifdef LISA_HASH
//-----------------------------------
uint64_t** cr_batch = (uint64_t**) malloc((mv->n)*sizeof(uint64_t*));
int* t_batch = (int*)malloc((mv->n)*sizeof(int));
uint64_t* minimizers = (uint64_t*) malloc((mv->n)*sizeof(uint64_t));
int64_t* lisa_pos = (int64_t*) malloc((max(32, (int)mv->n))* sizeof(int64_t));
for (size_t i = 0; i < mv->n; i++) {
mm128_t *p = &mv->a[i];
minimizers[i] = p->x>>8;
}
lh->mm_idx_get_batched(minimizers, mv->n, lisa_pos, cr_batch, t_batch);
//-----------------------------------
#endif
mm_seed_t *m;
size_t i;
int32_t k;
@@ -14,7 +45,12 @@ mm_seed_t *mm_seed_collect_all(void *km, const mm_idx_t *mi, const mm128_v *mv,
mm128_t *p = &mv->a[i];
uint32_t q_pos = (uint32_t)p->y, q_span = p->x & 0xff;
int t;
#ifdef LISA_HASH
t = t_batch[i];
cr = cr_batch[i];
#else
cr = mm_idx_get(mi, p->x>>8, &t);
#endif
if (t == 0) continue;
q = &m[k++];
q->q_pos = q_pos, q->q_span = q_span, q->cr = cr, q->n = t, q->seg_id = p->y >> 32;
@@ -22,7 +58,16 @@ mm_seed_t *mm_seed_collect_all(void *km, const mm_idx_t *mi, const mm128_v *mv,
if (i > 0 && p->x>>8 == mv->a[i - 1].x>>8) q->is_tandem = 1;
if (i < mv->n - 1 && p->x>>8 == mv->a[i + 1].x>>8) q->is_tandem = 1;
}
#ifdef LISA_HASH
free(cr_batch);
free(t_batch);
free(minimizers);
free(lisa_pos);
#endif
*n_m_ = k;
#ifdef MANUAL_PROFILING
minimizer_lookup_time += __rdtsc() - lookup_start;
#endif
return m;
}