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write to hifiasm read store

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This commit is contained in:
Heng Li
2020-03-26 14:23:17 -04:00
parent c3bbaa8a39
commit 0dd927bdce
8 changed files with 91 additions and 67 deletions
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4
Assembly.cpp
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@@ -265,7 +265,7 @@ void* Build_hash_table(void* arg)
}
///load read
compress_base(Get_READ(R_INF, curr_sub_block.read[i].ID),
ha_compress_base(Get_READ(R_INF, curr_sub_block.read[i].ID),
curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l,
&R_INF.N_site[curr_sub_block.read[i].ID], HPC_read.N_occ);
@@ -1170,7 +1170,7 @@ void* Save_corrected_reads(void* arg)
R_INF.read_length[i] = new_read_length;
compress_base(Get_READ(R_INF, i),
ha_compress_base(Get_READ(R_INF, i),
new_read, new_read_length,
&R_INF.N_site[i], N_occ);
}

3
Assembly.h
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@@ -8,9 +8,6 @@
#define Get_Cigar_Type(RECORD) (RECORD&3)
#define Get_Cigar_Length(RECORD) (RECORD>>2)
void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt);
void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab);
void Counting_multiple_thr();
void Build_hash_table_multiple_thr();
void Overlap_calculate_multipe_thr();

9
Makefile
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@@ -52,10 +52,11 @@ POA.o: kvec.h kdq.h CommandLines.h htab.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
Trio.o: khashl.h kthread.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
Trio.o: CommandLines.h htab.h
hist.o: htab.h
htab.o: kthread.h khashl.h kseq.h htab.h CommandLines.h
hist.o: htab.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
htab.o: kthread.h khashl.h kseq.h ksort.h htab.h Process_Read.h Overlaps.h
htab.o: kvec.h kdq.h CommandLines.h
kthread.o: kthread.h
main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
main.o: Assembly.h Levenshtein_distance.h htab.h
sketch.o: kvec.h htab.h
sys.o: htab.h
sketch.o: kvec.h htab.h Process_Read.h kseq.h Overlaps.h kdq.h CommandLines.h
sys.o: htab.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h

2
Process_Read.cpp
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@@ -590,7 +590,7 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
}\
i++;}\
void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ)
void ha_compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ)
{
///N_site_lis saves the pos of all Ns in this read
///N_site_lis[0] is the number of Ns

16
Process_Read.h
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@@ -18,11 +18,11 @@
#define IS_FULL(buffer) ((buffer.num >= buffer.size)?1:0)
#define IS_EMPTY(buffer) ((buffer.num == 0)?1:0)
///#define Get_READ_LENGTH(R_INF, ID) (R_INF.index[ID+1] - R_INF.index[ID])
#define Get_READ_LENGTH(R_INF, ID) R_INF.read_length[(ID)]
#define Get_NAME_LENGTH(R_INF, ID) (R_INF.name_index[(ID)+1] - R_INF.name_index[(ID)])
#define Get_READ_LENGTH(R_INF, ID) (R_INF).read_length[(ID)]
#define Get_NAME_LENGTH(R_INF, ID) ((R_INF).name_index[(ID)+1] - (R_INF).name_index[(ID)])
///#define Get_READ(R_INF, ID) R_INF.read + (R_INF.index[ID]>>2) + ID
#define Get_READ(R_INF, ID) R_INF.read_sperate[(ID)]
#define Get_NAME(R_INF, ID) R_INF.name + R_INF.name_index[(ID)]
#define Get_READ(R_INF, ID) (R_INF).read_sperate[(ID)]
#define Get_NAME(R_INF, ID) ((R_INF).name + (R_INF).name_index[(ID)])
KSEQ_INIT(gzFile, gzread)
@@ -139,8 +139,6 @@ typedef struct
extern All_reads R_INF;
void malloc_All_reads(All_reads* r);
typedef struct
{
kseq_t* read;
@@ -175,10 +173,12 @@ typedef struct
void init_R_buffer(int thread_num);
void init_All_reads(All_reads* r);
void malloc_All_reads(All_reads* r);
void* input_reads_muti_threads(void*);
void init_R_buffer_block(R_buffer_block* curr_sub_block);
int get_reads_mul_thread(R_buffer_block* curr_sub_block);
void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ);
void ha_insert_read_len(All_reads *r, int read_len, int name_len);
void ha_compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ);
void init_UC_Read(UC_Read* r);
void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID);
void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID);
@@ -196,6 +196,4 @@ void clear_R_buffer();
void init_gz_files(hifiasm_opt_t* asm_opt);
void destory_gz_files();
void ha_insert_read_len(All_reads *r, int read_len, int name_len);
#endif

111
htab.cpp
View File

@@ -9,8 +9,6 @@
#include "kseq.h"
#include "ksort.h"
#include "htab.h"
#include "Process_Read.h"
#include "CommandLines.h"
#define YAK_COUNTER_BITS 12
#define YAK_N_COUNTS (1<<YAK_COUNTER_BITS)
@@ -468,20 +466,25 @@ static void count_seq_buf_HPC(ch_buf_t *buf, int k, int p, int len, const char *
#define HAF_COUNT_EXACT 0x1
#define HAF_COUNT_ALL 0x2
#define HAF_RS_WRITE_LEN 0x4
#define HAF_RS_WRITE_SEQ 0x8
#define HAF_RS_READ 0x10
typedef struct { // global data structure for kt_pipeline()
const yak_copt_t *opt;
const void *flt_tab;
int flag, create_new, is_store;
uint64_t batch_offset;
uint64_t n_base;
uint64_t n_seq;
kseq_t *ks;
ha_ct_t *ct;
ha_pt_t *pt;
const All_reads *rs_in;
All_reads *rs_out;
} pl_data_t;
typedef struct { // data structure for each step in kt_pipeline()
pl_data_t *p;
uint64_t n_seq0;
int n_seq, m_seq, sum_len, nk;
int *len;
char **seq;
@@ -505,7 +508,7 @@ static void worker_for_mz(void *data, long i, int tid)
st_data_t *s = (st_data_t*)data;
ha_mz1_v *b = &s->mz_buf[tid];
s->mz_buf[tid].n = 0;
ha_sketch(s->seq[i], s->len[i], s->p->opt->w, s->p->opt->k, s->p->batch_offset + i, s->p->opt->is_HPC, b, s->p->flt_tab);
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);
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));
@@ -519,25 +522,42 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
st_data_t *s;
CALLOC(s, 1);
s->p = p;
while ((ret = kseq_read(p->ks)) >= 0) {
int l = p->ks->seq.l;
if (p->batch_offset + s->n_seq >= (1<<28) - 1) {
fprintf(stderr, "ERROR: this implementation supports no more than %d reads\n", (1<<28) - 1);
exit(1);
s->n_seq0 = p->n_seq;
if (p->rs_in && (p->flag & HAF_RS_READ)) {
} else {
while ((ret = kseq_read(p->ks)) >= 0) {
int l = p->ks->seq.l;
if (p->n_seq >= 1<<28) {
fprintf(stderr, "ERROR: this implementation supports no more than %d reads\n", 1<<28);
exit(1);
}
if (p->rs_out) {
if (p->flag & HAF_RS_WRITE_LEN) {
assert(p->n_seq == p->rs_out->total_reads);
ha_insert_read_len(p->rs_out, l, p->ks->name.l);
} else if (p->flag & HAF_RS_WRITE_SEQ) {
int i, n_N;
for (i = n_N = 0; i < l; ++i) // count number of ambiguous bases
if (seq_nt4_table[(uint8_t)p->ks->seq.s[i]] >= 4)
++n_N;
assert(l == (int)p->rs_out->read_length[p->n_seq]);
ha_compress_base(Get_READ(*p->rs_out, p->n_seq), p->ks->seq.s, l, &p->rs_out->N_site[p->n_seq], n_N);
}
}
if (s->n_seq == s->m_seq) {
s->m_seq = s->m_seq < 16? 16 : s->m_seq + (s->m_seq>>1);
REALLOC(s->len, s->m_seq);
REALLOC(s->seq, s->m_seq);
}
MALLOC(s->seq[s->n_seq], l);
memcpy(s->seq[s->n_seq], p->ks->seq.s, l);
s->len[s->n_seq++] = l;
++p->n_seq;
s->sum_len += l;
s->nk += l - p->opt->k + 1;
if (s->sum_len >= p->opt->chunk_size)
break;
}
p->n_base += l;
if (s->n_seq == s->m_seq) {
s->m_seq = s->m_seq < 16? 16 : s->m_seq + (s->m_seq>>1);
REALLOC(s->len, s->m_seq);
REALLOC(s->seq, s->m_seq);
}
MALLOC(s->seq[s->n_seq], l);
memcpy(s->seq[s->n_seq], p->ks->seq.s, l);
s->len[s->n_seq++] = l;
s->sum_len += l;
s->nk += l - p->opt->k + 1;
if (s->sum_len >= p->opt->chunk_size)
break;
}
if (s->sum_len == 0) free(s);
else return s;
@@ -601,17 +621,16 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
}
if (p->ct) p->ct->tot += n_ins;
if (p->pt) p->pt->tot_pos += n_ins;
p->batch_offset += s->n_seq;
free(s->buf);
fprintf(stderr, "[M::%s::%.3f*%.2f] processed %ld sequences; %ld %s in the hash table\n", __func__,
yak_realtime(), yak_cputime() / yak_realtime(), (long)p->batch_offset,
yak_realtime(), yak_cputime() / yak_realtime(), (long)s->n_seq0 + s->n_seq,
(long)(p->pt? p->pt->tot_pos : p->ct->tot), p->pt? "positions" : "distinct k-mers");
free(s);
}
return 0;
}
static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt_t *p0, ha_ct_t *c0, const void *flt_tab)
static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt_t *p0, ha_ct_t *c0, const void *flt_tab, All_reads *rs)
{
pl_data_t pl;
gzFile fp;
@@ -620,6 +639,11 @@ static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt
pl.ks = kseq_init(fp);
pl.flt_tab = flt_tab;
pl.opt = opt;
pl.flag = flag;
if (flag & (HAF_RS_WRITE_LEN|HAF_RS_WRITE_SEQ))
pl.rs_out = rs;
else if (flag & HAF_RS_READ)
pl.rs_in = rs;
if (p0) {
pl.pt = p0, pl.create_new = 0;
assert(p0->k == opt->k && p0->pre == opt->pre);
@@ -636,28 +660,26 @@ static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt
return pl.ct;
}
static ha_ct_t *yak_count_file(const yak_copt_t *opt, int flag, ha_pt_t *p0, int n_fn, char **fn, const void *flt_tab)
ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const void *flt_tab, All_reads *rs)
{
int i;
ha_ct_t *h = 0;
for (i = 0; i < n_fn; ++i)
h = yak_count(opt, fn[i], flag, p0, h, flt_tab);
if (h && opt->bf_shift > 0)
ha_ct_destroy_bf(h);
return h;
}
ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const void *flt_tab)
{
yak_copt_t opt;
ha_ct_t *h;
ha_ct_t *h = 0;
assert(!(flag & HAF_RS_WRITE_LEN) || !(flag & HAF_RS_WRITE_SEQ)); // not both
if (flag & HAF_RS_WRITE_LEN)
init_All_reads(rs);
else if (flag & HAF_RS_WRITE_SEQ)
malloc_All_reads(rs);
yak_copt_init(&opt);
opt.k = asm_opt->k_mer_length;
opt.is_HPC = !asm_opt->no_HPC;
opt.w = flag & HAF_COUNT_ALL? 1 : asm_opt->mz_win;
opt.bf_shift = flag & HAF_COUNT_EXACT? 0 : asm_opt->bf_shift;
opt.n_thread = asm_opt->thread_num;
h = yak_count_file(&opt, flag, p0, asm_opt->num_reads, asm_opt->read_file_names, flt_tab);
for (i = 0; i < asm_opt->num_reads; ++i)
h = yak_count(&opt, asm_opt->read_file_names[i], flag, p0, h, flt_tab, rs);
if (h && opt.bf_shift > 0)
ha_ct_destroy_bf(h);
return h;
}
@@ -704,13 +726,14 @@ void ha_ft_destroy(void *h)
* High-level interfaces *
*************************/
void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt)
void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt, All_reads *rs)
{
yak_ft_t *flt_tab;
int64_t cnt[YAK_N_COUNTS];
int peak_hom, peak_het, cutoff;
ha_ct_t *h;
h = ha_count(asm_opt, HAF_COUNT_ALL, NULL, NULL);
h = ha_count(asm_opt, HAF_COUNT_ALL|HAF_RS_WRITE_LEN, NULL, NULL, rs);
if (rs) fprintf(stderr, "%ld,%ld,%ld\n", (long)rs->total_reads, (long)rs->total_reads_bases, (long)rs->total_name_length);
ha_ct_hist(h, cnt, asm_opt->thread_num);
peak_hom = yak_analyze_count(YAK_N_COUNTS, cnt, &peak_het);
if (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);
@@ -724,13 +747,13 @@ void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt)
return (void*)flt_tab;
}
void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab, All_reads *rs)
{
int64_t cnt[YAK_N_COUNTS], tot_cnt;
int peak_hom, peak_het, i;
ha_ct_t *ct;
ha_pt_t *pt;
ct = ha_count(asm_opt, HAF_COUNT_EXACT, NULL, flt_tab);
ct = ha_count(asm_opt, HAF_COUNT_EXACT|HAF_RS_WRITE_SEQ, NULL, flt_tab, rs);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> counted %ld distinct minimizer k-mers\n", __func__,
yak_realtime(), yak_cputime() / yak_realtime(), (long)ct->tot);
ha_ct_hist(ct, cnt, asm_opt->thread_num);
@@ -740,7 +763,7 @@ void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
ha_ct_shrink(ct, 2, YAK_MAX_COUNT - 1, asm_opt->thread_num);
for (i = 2, tot_cnt = 0; i <= YAK_MAX_COUNT - 1; ++i) tot_cnt += cnt[i] * i;
pt = ha_pt_gen(ct, asm_opt->thread_num);
ha_count(asm_opt, HAF_COUNT_EXACT, pt, flt_tab);
ha_count(asm_opt, HAF_COUNT_EXACT, pt, flt_tab, rs);
assert((uint64_t)tot_cnt == pt->tot_pos);
ha_pt_sort(pt, asm_opt->thread_num);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> indexed %ld positions\n", __func__,

8
htab.h
View File

@@ -2,6 +2,8 @@
#define __HA_HTAB_H__
#define __STDC_LIMIT_MACROS
#include <stdint.h>
#include "Process_Read.h"
#include "CommandLines.h"
typedef struct {
uint64_t x;
@@ -16,12 +18,14 @@ typedef struct { uint32_t n, m; ha_mz1_t *a; } ha_mz1_v;
extern const unsigned char seq_nt4_table[256];
void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt, All_reads *rs);
void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab, All_reads *rs);
void trio_partition(void);
int ha_ft_isflt(const void *hh, uint64_t y);
void ha_ft_destroy(void *h);
void ha_idx_destroy(void *h);
void trio_partition(void);
double yak_cputime(void);
void yak_reset_realtime(void);
double yak_realtime(void);

5
main.cpp
View File

@@ -17,13 +17,14 @@ int main(int argc, char *argv[])
if (!CommandLine_process(argc, argv, &asm_opt)) return 1;
yak_reset_realtime();
flt_tab = ha_gen_flt_tab(&asm_opt);
idx = ha_gen_mzidx(&asm_opt, flt_tab);
flt_tab = ha_gen_flt_tab(&asm_opt, &R_INF);
idx = ha_gen_mzidx(&asm_opt, flt_tab, &R_INF);
ha_idx_destroy(idx);
ha_ft_destroy(flt_tab);
if (0) {
Correct_Reads(asm_opt.number_of_round);
}
destory_All_reads(&R_INF);
destory_opt(&asm_opt);
fprintf(stderr, "[M::%s] Version: %s\n", __func__, "dummy");
fprintf(stderr, "[M::%s] CMD:", __func__);