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a bit refactoring for the next change

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This commit is contained in:
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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1
CommandLines.cpp
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@@ -102,6 +102,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->k_mer_length = 51;
asm_opt->mz_win = 51;
asm_opt->bf_shift = 37;
asm_opt->max_kmer_cnt = 4000;
asm_opt->high_factor = 5.0;
asm_opt->max_ov_diff_ec = 0.04;
asm_opt->max_ov_diff_final = 0.03;

1
CommandLines.h
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@@ -35,6 +35,7 @@ typedef struct {
int k_mer_length;
int mz_win;
int bf_shift;
int max_kmer_cnt;
double high_factor; // coverage cutoff set to high_factor*hom_cov
double max_ov_diff_ec;
double max_ov_diff_final;

2
anchor.cpp
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@@ -73,7 +73,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
rlen = Get_READ_LENGTH(R_INF, rid); // read length
// get the list of anchors
ha_sketch_query(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag, dbg_ct);
ha_sketch(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag, dbg_ct);
// minimizer of queried read
if (ab->mz.m > ab->old_mz_m) {
ab->old_mz_m = ab->mz.m;

29
htab.cpp
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@@ -1,4 +1,3 @@
#include <stdint.h>
#include <zlib.h>
#include <stdio.h>
#include <string.h>
@@ -557,7 +556,7 @@ static void worker_for_mz(void *data, long i, int tid)
ha_mz1_v *b = &s->mz_buf[tid];
s->mz_buf[tid].n = 0;
///s->p->opt->w = 51, s->p->opt->k
ha_sketch_query(s->seq[i], s->len[i], s->p->opt->w, s->p->opt->k, s->n_seq0 + i, s->p->opt->is_HPC, b, s->p->flt_tab, 0, 0);
ha_sketch(s->seq[i], s->len[i], s->p->opt->w, s->p->opt->k, s->n_seq0 + i, s->p->opt->is_HPC, b, s->p->flt_tab, 0, 0);
s->mz[i].n = s->mz[i].m = b->n;
MALLOC(s->mz[i].a, b->n);
memcpy(s->mz[i].a, b->a, b->n * sizeof(ha_mz1_t));
@@ -803,12 +802,15 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const voi
* High count filter table *
***************************/
// Warning: the max count is 32767
KHASHL_MAP_INIT(static klib_unused, yak_ft_t, yak_ft, uint64_t, int16_t, kh_hash_dummy, kh_eq_generic)
static yak_ft_t *gen_hh(const ha_ct_t *h)
static yak_ft_t *gen_hh(const ha_ct_t *h, int max_cnt)
{
int i;
yak_ft_t *hh;
if (max_cnt > YAK_MAX_COUNT - 1) max_cnt = YAK_MAX_COUNT - 1;
if (max_cnt > INT16_MAX - 1) max_cnt = INT16_MAX - 1;
hh = yak_ft_init();
yak_ft_resize(hh, h->tot * 2);
for (i = 0; i < 1<<h->pre; ++i) {
@@ -819,28 +821,22 @@ static yak_ft_t *gen_hh(const ha_ct_t *h)
uint64_t y = kh_key(ht, k) >> h->pre << YAK_COUNTER_BITS | i;
int absent;
l = yak_ft_put(hh, y, &absent);
if (absent)
kh_val(hh, l) = kh_key(ht, k)&YAK_MAX_COUNT;
if (absent) {
int cnt = kh_key(ht, k) & YAK_MAX_COUNT;
kh_val(hh, l) = cnt > max_cnt? INT16_MAX : cnt;
}
}
}
}
return hh;
}
int ha_ft_isflt(const void *hh, uint64_t y)
int32_t ha_ft_cnt(const void *hh, uint64_t y)
{
yak_ft_t *h = (yak_ft_t*)hh;
khint_t k;
k = yak_ft_get(h, y);
return k == kh_end(h)? 0 : 1;
}
int ha_ft_cnt(const void *hh, uint64_t y)
{
yak_ft_t *h = (yak_ft_t*)hh;
khint_t k;
k = yak_ft_get(h, y);
return k == kh_end(h)? 0 : kh_val(h, k);
return k == kh_end(h)? 0 : kh_val(h, k) == INT16_MAX? INT32_MAX : kh_val(h, k);
}
void ha_ft_destroy(void *h)
@@ -906,7 +902,7 @@ void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs, int *hom_cov, int i
if (cutoff > YAK_MAX_COUNT - 1) cutoff = YAK_MAX_COUNT - 1;
}
ha_ct_shrink(h, cutoff, YAK_MAX_COUNT, asm_opt->thread_num);
flt_tab = gen_hh(h);
flt_tab = gen_hh(h, asm_opt->max_kmer_cnt);
ha_ct_destroy(h);
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> filtered out %ld k-mers occurring %d or more times\n", __func__,
yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb(), (long)kh_size(flt_tab), cutoff);
@@ -970,7 +966,6 @@ int query_ct_index(void* ct_idx, uint64_t hash)
return kh_key(g->h, k)&YAK_MAX_COUNT;
}
int write_ct_index(void *i_ct_idx, char* file_name)
{
char* gfa_name = (char*)malloc(strlen(file_name)+25);

6
htab.h
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@@ -31,9 +31,8 @@ extern void *ha_flt_tab_hp;
extern ha_pt_t *ha_idx_hp;
extern void *ha_ct_table;
void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs, int *hom_cov, int is_hp_mode);
int ha_ft_cnt(const void *hh, uint64_t y);
int32_t ha_ft_cnt(const void *hh, uint64_t y);
void ha_ft_destroy(void *h);
ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_from_store, int is_hp_mode, All_reads *rs, int *hom_cov, int *het_cov);
@@ -59,8 +58,7 @@ double yak_cpu_usage(void);
void ha_triobin(const hifiasm_opt_t *opt);
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);
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);
int ha_analyze_count(int n_cnt, int start_cnt, const int64_t *cnt, int *peak_het);
static inline uint64_t yak_hash64(uint64_t key, uint64_t mask) // invertible integer hash function

16
sketch.cpp
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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;
}