xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-01 07:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

code clean

Browse Source
This commit is contained in:
chhylp123
2022-11-17 09:31:56 -05:00
parent 2c7b164f11
commit 9831afaf26
12 changed files with 1296 additions and 127 deletions
Download Patch File Download Diff File Expand all files Collapse all files
inter.cpp
+21 -15
View File
@@ -4876,7 +4876,8 @@ void update_ul_vec_t_ug(const ul_idx_t *uref, ul_vec_t *rch, vec_mg_lchain_t *uc
rch->bb.a[rch->bb.a[k].pidx].aidx = k;
}
// fprintf(stderr, "+ulid->%ld\n", ulid);
uint32_t sp = (uint32_t)-1, ep = (uint32_t)-1; k = l/**a_n - 1**/;///start from the max chain
uint32_t sp = (uint32_t)-1, ep = (uint32_t)-1, ch_n = 0;
k = l/**a_n - 1**/;///start from the max chain
for (l = 0; k >= 0; ) {
if(sp == (uint32_t)-1 || rch->bb.a[k].qe <= sp) {
if(sp != (uint32_t)-1) l += ep - sp;
@@ -4886,6 +4887,7 @@ void update_ul_vec_t_ug(const ul_idx_t *uref, ul_vec_t *rch, vec_mg_lchain_t *uc
}
if(rch->bb.a[k].pidx == (uint32_t)-1) k = -1;
else k = rch->bb.a[k].pidx;
ch_n++;
}
rch->dd = 0;
@@ -4897,8 +4899,9 @@ void update_ul_vec_t_ug(const ul_idx_t *uref, ul_vec_t *rch, vec_mg_lchain_t *uc
rch->dd = 1;
} else if(l < ((int64_t)rch->rlen)*0.001) {
rch->dd = 2;
} else if(ch_n < rch->bb.n) {///multiple chain, might be useful for the scaffolding
rch->dd = 3;
}
// fprintf(stderr, "[M::%s::] rch->dd::%u, rch->bb.n::%u\n",
// __func__, rch->dd, (uint32_t)rch->bb.n);
}
@@ -8975,9 +8978,12 @@ static void worker_for_ul_rescall_alignment(void *data, long i, int tid) // call
// b->num_correct_base += b->correct.corrected_base;
// b->num_recorrect_base += b->round2.dumy.corrected_base;
if(UL_INF.a[s->id+i].dd) {
free(s->seq[i]); s->seq[i] = NULL; b->num_correct_base++;
if(UL_INF.a[s->id+i].dd == 1 || UL_INF.a[s->id+i].dd == 2) {
b->num_correct_base++;
}
if(UL_INF.a[s->id+i].dd != 3) {
free(s->seq[i]); s->seq[i] = NULL;
}
s->hab[tid]->num_read_base++;
// fprintf(stderr, "[M::%s] rid:%ld, dd:%u\n", __func__, s->id+i, UL_INF.a[s->id+i].dd);
// int64_t mem[6], mem_hab[6];
@@ -9364,9 +9370,9 @@ static void *worker_ul_scall_pipeline(void *data, int step, void *in) // callbac
// s->hab[i] = ha_ovec_buf_init(NULL, 0, 0, 1);
s->hab[i] = ha_ovec_init(0, 0, 1);
}
fprintf(stderr, "[M::%s::Start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
// fprintf(stderr, "[M::%s::Start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
kt_for(p->n_thread, worker_for_ul_scall_alignment, s, s->n);
fprintf(stderr, "[M::%s::Done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
// fprintf(stderr, "[M::%s::Done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
///debug
/**
uint64_t i;
@@ -9408,7 +9414,7 @@ static void *worker_ul_scall_pipeline(void *data, int step, void *in) // callbac
p->num_bases += s->num_bases;
p->num_corrected_bases += s->num_corrected_bases;
p->num_recorrected_bases += s->num_recorrected_bases;
fprintf(stderr, "[M::%s::dump_start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
// fprintf(stderr, "[M::%s::dump_start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
for (i = 0; i < p->n_thread; ++i) {
push_uc_block_t(s->uopt, &(s->ll[i].tk), s->seq, s->len, s->id);
free(s->ll[i].tk.a);
@@ -9420,7 +9426,7 @@ static void *worker_ul_scall_pipeline(void *data, int step, void *in) // callbac
}
free(s->seq[i]);
}
fprintf(stderr, "[M::%s::dump_done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
// fprintf(stderr, "[M::%s::dump_done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
/**
for (i = 0; i < (uint64_t)s->n; ++i) {
///debug
@@ -9495,10 +9501,10 @@ static void *worker_ul_rescall_pipeline(void *data, int step, void *in) // callb
for (i = 0; i < p->n_thread; ++i) {
s->hab[i] = ha_ovec_init(0, 0, 1); s->buf[i] = mg_tbuf_init();
}
fprintf(stderr, "[M::%s::Start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
// fprintf(stderr, "[M::%s::Start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
kt_for(p->n_thread, worker_for_ul_rescall_alignment, s, s->n);
fprintf(stderr, "[M::%s::Done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
get_utepdat_t_mem(s, 1);
// fprintf(stderr, "[M::%s::Done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
// get_utepdat_t_mem(s, 1);
for (i = 0; i < p->n_thread; ++i) {
p->num_bases += s->hab[i]->num_read_base;
@@ -9514,10 +9520,10 @@ static void *worker_ul_rescall_pipeline(void *data, int step, void *in) // callb
return s;
} else if (step == 2) { // step 3: dump
utepdat_t *s = (utepdat_t*)in; int64_t i, rid;
fprintf(stderr, "[M::%s::dump_start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
// fprintf(stderr, "[M::%s::dump_start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
for (i = 0; i < s->n; ++i) {
rid = s->id + i;
if(UL_INF.a[rid].dd == 0 && p->ucr_s && p->ucr_s->flag == 1) {
if(UL_INF.a[rid].dd == 3 && p->ucr_s && p->ucr_s->flag == 1) {///for the scaffolding
assert(s->seq[i]);
// if(s->seq[i] == NULL) fprintf(stderr, "[M::%s::]rid->%ld, len->%lu\n", __func__, rid, s->len[i]);
///for debug interval
@@ -9526,7 +9532,7 @@ static void *worker_ul_rescall_pipeline(void *data, int step, void *in) // callb
// if(UL_INF.a[rid].dd) fprintf(stderr, "rid->%ld\n", rid);
free(s->seq[i]);
}
fprintf(stderr, "[M::%s::dump_done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
// fprintf(stderr, "[M::%s::dump_done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
free(s->len); free(s->seq); free(s);
}
return 0;
@@ -14752,7 +14758,7 @@ ma_ug_t *ul_realignment(const ug_opt_t *uopt, asg_t *sg, uint32_t double_check_c
mg_idxopt_t opt; uldat_t sl;
int32_t cutoff;
char* gfa_name = NULL; MALLOC(gfa_name, strlen(asm_opt.output_file_name)+50);
sprintf(gfa_name, "%s.re", asm_opt.output_file_name);
sprintf(gfa_name, "%s.%s", asm_opt.output_file_name, HA_RE_UL_ID);
init_aux_table(); ha_opt_update_cov(&asm_opt, asm_opt.hom_cov);
cutoff = REA_ALIGN_CUTOFF;