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read from read store

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This commit is contained in:
Heng Li
2020-03-26 15:17:49 -04:00
parent 0dd927bdce
commit 387d6336d8
5 changed files with 52 additions and 24 deletions
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Process_Read.cpp
+1 -1
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@@ -511,7 +511,7 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
}
void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID)
void recover_UC_Read(UC_Read* r, const All_reads *R_INF, uint64_t ID)
{
r->length = Get_READ_LENGTH((*R_INF), ID);
uint8_t* src = Get_READ((*R_INF), ID);
Process_Read.h
+1 -1
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@@ -180,7 +180,7 @@ int get_reads_mul_thread(R_buffer_block* curr_sub_block);
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(UC_Read* r, const All_reads *R_INF, uint64_t ID);
void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID);
void recover_UC_Read_sub_region(char* r, long long start_pos, long long length, uint8_t strand, All_reads* R_INF, long long ID);
void destory_UC_Read(UC_Read* r);
htab.cpp
+48 -20
View File
@@ -476,6 +476,7 @@ typedef struct { // global data structure for kt_pipeline()
int flag, create_new, is_store;
uint64_t n_seq;
kseq_t *ks;
UC_Read ucr;
ha_ct_t *ct;
ha_pt_t *pt;
const All_reads *rs_in;
@@ -524,6 +525,24 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
s->p = p;
s->n_seq0 = p->n_seq;
if (p->rs_in && (p->flag & HAF_RS_READ)) {
while (p->n_seq < p->rs_in->total_reads) {
int l;
recover_UC_Read(&p->ucr, p->rs_in, p->n_seq);
l = p->ucr.length;
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->ucr.seq, l);
s->len[s->n_seq++] = l;
++p->n_seq;
s->sum_len += l;
s->nk += l >= p->opt->k? l - p->opt->k + 1 : 0;
if (s->sum_len >= p->opt->chunk_size)
break;
}
} else {
while ((ret = kseq_read(p->ks)) >= 0) {
int l = p->ks->seq.l;
@@ -537,10 +556,10 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
ha_insert_read_len(p->rs_out, l, p->ks->name.l);
} else if (p->flag & HAF_RS_WRITE_SEQ) {
int i, n_N;
assert(l == (int)p->rs_out->read_length[p->n_seq]);
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);
}
}
@@ -554,7 +573,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
s->len[s->n_seq++] = l;
++p->n_seq;
s->sum_len += l;
s->nk += l - p->opt->k + 1;
s->nk += l >= p->opt->k? l - p->opt->k + 1 : 0;
if (s->sum_len >= p->opt->chunk_size)
break;
}
@@ -632,18 +651,22 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
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)
{
int read_rs = (rs && (flag & HAF_RS_READ));
pl_data_t pl;
gzFile fp;
if ((fp = gzopen(fn, "r")) == 0) return 0;
gzFile fp = 0;
memset(&pl, 0, sizeof(pl_data_t));
pl.ks = kseq_init(fp);
if (read_rs) {
pl.rs_in = rs;
init_UC_Read(&pl.ucr);
} else {
if ((fp = gzopen(fn, "r")) == 0) return 0;
pl.ks = kseq_init(fp);
}
if (rs && (flag & (HAF_RS_WRITE_LEN|HAF_RS_WRITE_SEQ)))
pl.rs_out = rs;
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);
@@ -655,8 +678,12 @@ static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt
pl.ct = ha_ct_init(opt->k, opt->pre, opt->bf_n_hash, opt->bf_shift);
}
kt_pipeline(3, worker_count, &pl, 3);
kseq_destroy(pl.ks);
gzclose(fp);
if (read_rs) {
destory_UC_Read(&pl.ucr);
} else {
kseq_destroy(pl.ks);
gzclose(fp);
}
return pl.ct;
}
@@ -666,10 +693,12 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const voi
yak_copt_t opt;
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);
if (rs) {
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;
@@ -733,7 +762,6 @@ void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt, All_reads *rs)
int peak_hom, peak_het, cutoff;
ha_ct_t *h;
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);
@@ -747,13 +775,13 @@ void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt, All_reads *rs)
return (void*)flt_tab;
}
void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab, All_reads *rs)
void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_from_store, All_reads *rs)
{
int64_t cnt[YAK_N_COUNTS], tot_cnt;
int peak_hom, peak_het, i;
int peak_hom, peak_het, i, extra_flag = read_from_store? HAF_RS_READ : HAF_RS_WRITE_SEQ;
ha_ct_t *ct;
ha_pt_t *pt;
ct = ha_count(asm_opt, HAF_COUNT_EXACT|HAF_RS_WRITE_SEQ, NULL, flt_tab, rs);
ct = ha_count(asm_opt, HAF_COUNT_EXACT|extra_flag, 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);
@@ -763,7 +791,7 @@ void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab, All_reads
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, rs);
ha_count(asm_opt, HAF_COUNT_EXACT|HAF_RS_READ, 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__,
htab.h
+1 -1
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@@ -19,7 +19,7 @@ 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 *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_from_store, All_reads *rs);
void trio_partition(void);
int ha_ft_isflt(const void *hh, uint64_t y);
main.cpp
+1 -1
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@@ -18,7 +18,7 @@ int main(int argc, char *argv[])
yak_reset_realtime();
flt_tab = ha_gen_flt_tab(&asm_opt, &R_INF);
idx = ha_gen_mzidx(&asm_opt, flt_tab, &R_INF);
idx = ha_gen_mzidx(&asm_opt, flt_tab, 0, &R_INF);
ha_idx_destroy(idx);
ha_ft_destroy(flt_tab);
if (0) {