xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-01 00:38:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge branch 'master' into dev-lh3

Browse Source
This commit is contained in:
Heng Li
2021-03-02 19:27:44 -05:00
parent 205eadf346 d2ca12604b
commit 8e98fb2276
17 changed files with 16486 additions and 4393 deletions
Download Patch File Download Diff File Expand all files Collapse all files
htab.cpp
+56 -9
View File
@@ -48,6 +48,7 @@ typedef struct {
int32_t pre;
int32_t n_thread;
int64_t chunk_size;
int adaLen;
} yak_copt_t;
void yak_copt_init(yak_copt_t *o)
@@ -596,7 +597,9 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
}
} else {
while ((ret = kseq_read(p->ks)) >= 0) {
int l = p->ks->seq.l;
int l = (int)(p->ks->seq.l) - (int)(p->opt->adaLen) - (int)(p->opt->adaLen);
if(l <= 0) continue;
if (p->n_seq >= 1<<28) {
fprintf(stderr, "ERROR: this implementation supports no more than %d reads\n", 1<<28);
exit(1);
@@ -610,9 +613,9 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
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)
if (seq_nt4_table[(uint8_t)p->ks->seq.s[i+p->opt->adaLen]] >= 4)
++n_N;
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);
ha_compress_base(Get_READ(*p->rs_out, p->n_seq), p->ks->seq.s+p->opt->adaLen, l, &p->rs_out->N_site[p->n_seq], n_N);
memcpy(&p->rs_out->name[p->rs_out->name_index[p->n_seq]], p->ks->name.s, p->ks->name.l);
}
}
@@ -623,7 +626,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
REALLOC(s->seq, s->m_seq);
}
MALLOC(s->seq[s->n_seq], l);
memcpy(s->seq[s->n_seq], p->ks->seq.s, l);
memcpy(s->seq[s->n_seq], p->ks->seq.s+p->opt->adaLen, l);
s->len[s->n_seq++] = l;
++p->n_seq;
s->sum_len += l;
@@ -719,6 +722,48 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
return 0;
}
void debug_adapter(const hifiasm_opt_t *asm_opt, All_reads *rs)
{
int ret;
uint32_t i, m, pass, unpass;
gzFile fp = 0;
kseq_t *ks = NULL;
UC_Read ucr;
init_UC_Read(&ucr);
for (i = m = pass = unpass = 0; i < (uint32_t)asm_opt->num_reads; ++i)
{
if ((fp = gzopen(asm_opt->read_file_names[i], "r")) == 0) continue;
ks = kseq_init(fp);
while ((ret = kseq_read(ks)) >= 0)
{
int l = ks->seq.l;
if((l - asm_opt->adapterLen*2) <= 0) continue;
recover_UC_Read(&ucr, rs, m);
fprintf(stderr, "l: %d, ucr.length: %lld, asm_opt->adapterLen: %d\n",
l, ucr.length, asm_opt->adapterLen);
if(memcmp(ucr.seq, ks->seq.s+asm_opt->adapterLen, ucr.length) == 0)
{
pass++;
}
else
{
unpass++;
}
m++;
}
kseq_destroy(ks);
gzclose(fp);
ks = NULL;
fp = 0;
}
destory_UC_Read(&ucr);
fprintf(stderr, "[M::%s::# reads: %u, # pass: %u, # unpass: %u\n]", __func__, m, pass, unpass);
exit(1);
}
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, int64_t *n_seq)
{
///for 0-th counting, flag = HAF_COUNT_ALL|HAF_RS_WRITE_LEN|HAF_CREATE_NEW
@@ -791,6 +836,7 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const voi
///for ha_pt_gen, shoud be 0
opt.bf_shift = flag & HAF_COUNT_EXACT? 0 : asm_opt->bf_shift;
opt.n_thread = asm_opt->thread_num;
opt.adaLen = asm_opt->adapterLen;
///asm_opt->num_reads is the number of fastq files
for (i = 0; i < asm_opt->num_reads; ++i)
h = yak_count(&opt, asm_opt->read_file_names[i], flag|HAF_CREATE_NEW, p0, h, flt_tab, rs, &n_seq);
@@ -1008,16 +1054,17 @@ int load_ct_index(void **i_ct_idx, char* file_name)
}
ha_ct_t** ct_idx = (ha_ct_t**)i_ct_idx;
double index_time = 0;
uint64_t flag = 0;
int i;
ha_ct_t *h = 0;
ha_ct1_t *g;
CALLOC(h, 1);
fread(&h->k, sizeof(h->k), 1, fp);
fread(&h->pre, sizeof(h->pre), 1, fp);
fread(&h->n_hash, sizeof(h->n_hash), 1, fp);
fread(&h->n_shift, sizeof(h->n_shift), 1, fp);
fread(&h->tot, sizeof(h->tot), 1, fp);
flag += fread(&h->k, sizeof(h->k), 1, fp);
flag += fread(&h->pre, sizeof(h->pre), 1, fp);
flag += fread(&h->n_hash, sizeof(h->n_hash), 1, fp);
flag += fread(&h->n_shift, sizeof(h->n_shift), 1, fp);
flag += fread(&h->tot, sizeof(h->tot), 1, fp);
CALLOC(h->h, 1<<h->pre);