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a bit refactoring for the next change

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Heng Li
2020-10-29 18:24:47 -04:00
parent ef8c047559
commit f37c4e29fa
6 changed files with 26 additions and 29 deletions
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sketch.cpp
+9 -7
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@@ -36,7 +36,7 @@ static inline int tq_shift(tiny_queue_t *q)
* @param is_hpc homopolymer-compressed or not
* @param p minimizers
*/
void ha_sketch_query(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, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct)
{ ///in default, w = 51, k = 51, is_hpc = 1
/**
uint64_t x;
@@ -57,8 +57,7 @@ void ha_sketch_query(const char *str, int len, int w, int k, uint32_t rid, int i
memset(k_flag->a.a, 0, k_flag->a.n);
}
///sizeof(ha_mz1_t) = 16
memset(buf, 0xff, w * 16);
memset(buf, 0xff, w * sizeof(ha_mz1_t));
memset(&tq, 0, sizeof(tiny_queue_t));
///len/w is the evaluated minimizer numbers
kv_resize(ha_mz1_t, *p, p->n + len/w);
@@ -97,12 +96,13 @@ void ha_sketch_query(const char *str, int len, int w, int k, uint32_t rid, int i
++l;
if (l >= k && kmer_span < 256) {
uint64_t y;
int filtered = 0;
int32_t cnt = 0, filtered = 0;
y = yak_hash64_64(kmer[z<<1|0]) + yak_hash64_64(kmer[z<<1|1]);
if (hf != 0) filtered = (ha_ft_cnt(hf, y) > 0);
if (hf != 0) cnt = ha_ft_cnt(hf, y);
filtered = (cnt > 0);
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 == 0)
info.x = y, info.rid = rid, info.pos = i, info.rev = z, info.span = kmer_span;
if (cnt < 1<<28 && filtered == 0)
info.x = y, info.rid = cnt, info.pos = i, info.rev = z, info.span = kmer_span;
if (k_flag != NULL) k_flag->a.a[i]++;
if (k_flag != NULL && filtered > 0) k_flag->a.a[i]++;
}
@@ -150,4 +150,6 @@ void ha_sketch_query(const char *str, int len, int w, int k, uint32_t rid, int i
}
if (min.x != UINT64_MAX)
kv_push(ha_mz1_t, *p, min);
for (i = 0; i < (int)p->n; ++i) // populate .rid as this was keeping counts
p->a[i].rid = rid;
}