xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-29 23:38:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

correction

Browse Source
This commit is contained in:
chhylp123
2021-05-11 13:01:06 -04:00
parent 7918396d21
commit 4105dd360e
6 changed files with 711 additions and 41 deletions
Download Patch File Download Diff File Expand all files Collapse all files
hic.cpp
+47 -7
View File
@@ -15151,6 +15151,7 @@ ps_t* init_ps_t(uint64_t seed, uint64_t n)
ps_t *s = NULL; CALLOC(s, 1);
s->xs = seed;
CALLOC(s->s, n);
s->n = n;
return s;
}
@@ -15424,6 +15425,39 @@ void print_kv_u_trans_t(kv_u_trans_t *ta)
fprintf(stderr, "[M::%s::] \n", __func__);
}
void write_ps_t(ps_t *s, const char *fn)
{
char *buf = (char*)calloc(strlen(fn) + 25, 1);
sprintf(buf, "%s.hic.pst.bin", fn);
FILE* fp = fopen(buf, "w");
fwrite(&(s->xs), sizeof(s->xs), 1, fp);
fwrite(&(s->n), sizeof(s->n), 1, fp);
fwrite(s->s, sizeof(int8_t), s->n, fp);
fclose(fp);
free(buf);
}
int load_ps_t(ps_t **s, const char *fn)
{
uint64_t flag = 0;
char *buf = (char*)calloc(strlen(fn) + 25, 1);
sprintf(buf, "%s.hic.pst.bin", fn);
FILE* fp = NULL;
fp = fopen(buf, "r");
if(!fp) return 0;
CALLOC(*s, 1);
flag += fread(&((*s)->xs), sizeof((*s)->xs), 1, fp);
flag += fread(&((*s)->n), sizeof((*s)->n), 1, fp);
MALLOC((*s)->s, (*s)->n);
flag += fread((*s)->s, sizeof(int8_t), (*s)->n, fp);
fclose(fp);
free(buf);
return 1;
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt)
{
double index_time = yak_realtime();
@@ -15456,20 +15490,24 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
bubble_type bub;
kv_u_trans_t k_trans;
kv_init(k_trans); kv_init(k_trans.idx);
ps_t *s = init_ps_t(11, idx->ug->g->n_seq);
ps_t *s = NULL;
mb_nodes_t u;
kv_init(u.bid); kv_init(u.idx); kv_init(u.u);
memset(&bub, 0, sizeof(bubble_type));
bub.round_id = 0; bub.n_round = asm_opt.n_weight;
resolve_tangles_hic(idx, &bub, &sl.hits, &k_trans);
measure_distance(idx, idx->ug, &sl.hits, &link, &bub, &(idx->t_ch->k_trans));
if((asm_opt.flag & HA_F_VERBOSE_GFA) && load_ps_t(&s, asm_opt.output_file_name))
{
bub.round_id = bub.n_round;
label_unitigs_sm(s->s, idx->ug);
goto skip_flipping;
}
s = init_ps_t(11, idx->ug->g->n_seq);
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
// identify_bubbles(idx->ug, &bub, idx->t_ch->is_r_het, &(idx->t_ch->k_trans));
if(bub.round_id == 0)
{
resolve_tangles_hic(idx, &bub, &sl.hits, &k_trans);
measure_distance(idx, idx->ug, &sl.hits, &link, &bub, &(idx->t_ch->k_trans));
}
renew_kv_u_trans(&k_trans, &link, &sl.hits, &(idx->t_ch->k_trans), idx, &bub, s->s, 0);
// if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s);
// update_trans_g(idx, &k_trans, &bub);
@@ -15493,7 +15531,9 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
label_unitigs(&(hap.g_p), idx->ug);
**/
}
write_ps_t(s, asm_opt.output_file_name);
skip_flipping:
verbose_het_stat(&bub);
horder_t *ho = init_horder_t(&sl.hits, idx->uID_bits, idx->pos_mode, idx->read_g, idx->ug, &bub, opt);