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fix scaf bugs

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chhylp123
2024-04-27 07:58:49 -04:00
parent 1ac574adc7
commit 358b090e20
5 changed files with 297 additions and 65 deletions
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inter.cpp
+22 -16
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@@ -412,6 +412,7 @@ typedef struct { // global data structure for kt_pipeline()
kv_u_trans_t *ta;
uint64_t mm;
uint64_t soff;
uint64_t is_exact;
} ctdat_t;
@@ -4966,6 +4967,10 @@ void fill_unaligned_alignments(ma_ug_t *ug, mg_lchain_t *a, int64_t a_n, int64_t
}
}
void sort_uc_block_qe(uc_block_t* a, uint64_t a_n) {
radix_sort_uc_block_t_qe_srt(a, a + a_n);
}
void update_ul_vec_t_ug(const ul_idx_t *uref, ul_vec_t *rch, vec_mg_lchain_t *uc, int64_t ulid)
{
int64_t k, ucn = uc->n, a_n, m, l, lk; ma_ug_t *ug = uref->ug; mg_lchain_t *ix, *a; uc_block_t *z;
@@ -16802,7 +16807,7 @@ uint64_t gen_trans_ovlp_scaf(ma_ug_t *gfa, u_trans_t *map, uc_block_t *qin, uc_b
return 1;
}
void extract_trans_scaf_res_t(uc_block_t *qin, const ul_idx_t *uref, scaf_res_t *ref_sc, ma_ug_t *gfa, kv_u_trans_t *ta, uint32_t avid, kv_ul_ov_t *res)
void extract_trans_scaf_res_t(uc_block_t *qin, const ul_idx_t *uref, scaf_res_t *ref_sc, ma_ug_t *gfa, kv_u_trans_t *ta, uint32_t avid, uint32_t is_exact, kv_ul_ov_t *res)
{
utg_rid_dt *a; uint64_t i, a_n; uc_block_t *rin;
u_trans_t *u; uint64_t k, u_n;
@@ -16812,6 +16817,7 @@ void extract_trans_scaf_res_t(uc_block_t *qin, const ul_idx_t *uref, scaf_res_t
u = u_trans_a(*ta, qin->hid);
u_n = u_trans_n(*ta, qin->hid);
for (k = 0; k < u_n; k++) {
if(is_exact && u[k].f != RC_0 && u[k].f != RC_1) continue;
// fprintf(stderr, "+[M::%s] utg%.6u%c->utg%.6u%c, q::[%u, %u), %c, t::[%u, %u)\n", __func__, qin->hid+1, "lc"[gfa->u.a[qin->hid].circ], u[k].tn+1, "lc"[gfa->u.a[u[k].tn].circ], u[k].qs, u[k].qe, "+-"[u[k].rev], u[k].ts, u[k].te);
a = get_r_ug_region(uref->r_ug, &a_n, u[k].tn);
for (i = 0; i < a_n; i++) {
@@ -16827,7 +16833,7 @@ void extract_trans_scaf_res_t(uc_block_t *qin, const ul_idx_t *uref, scaf_res_t
}
}
void cl_trans_gen(uint32_t qid, uint32_t qlen, ul_vec_t *qstr, kv_ul_ov_t *res, const ul_idx_t *uref, ma_ug_t *ref, scaf_res_t *ref_sc, ma_ug_t *gfa, bubble_type *bub, kv_u_trans_t *ta, uint32_t is_self)
void cl_trans_gen(uint32_t qid, uint32_t qlen, ul_vec_t *qstr, kv_ul_ov_t *res, const ul_idx_t *uref, ma_ug_t *ref, scaf_res_t *ref_sc, ma_ug_t *gfa, bubble_type *bub, kv_u_trans_t *ta, uint32_t is_self, uint32_t is_exact)
{
uint64_t k, l, m = 0, mi, z, zn, a_n, bid, nw; uc_block_t *a; uint32_t avid = ((is_self)?(qid):((uint32_t)-1));
res->n = 0;
@@ -16882,7 +16888,7 @@ void cl_trans_gen(uint32_t qid, uint32_t qlen, ul_vec_t *qstr, kv_ul_ov_t *res,
if(extract_scaf_res_t(&(qstr->bb.a[z]), uref, ref_sc, avid, res)) continue;
///trans match
extract_trans_scaf_res_t(&(qstr->bb.a[z]), uref, ref_sc, gfa, ta, avid, res);
extract_trans_scaf_res_t(&(qstr->bb.a[z]), uref, ref_sc, gfa, ta, avid, is_exact, res);
}
}
@@ -17159,7 +17165,7 @@ double diff_ec_ul, double ovlp_max, double unmatch_max, int64_t qlen, int64_t tl
return 1;
}
void ctg_trans_gp_chain(uint32_t qid, kv_ul_ov_t *res, const ul_idx_t *uref, const ug_opt_t *uopt, int64_t bw, double diff_ec_ul, int64_t qlen, Chain_Data* dp, ma_ug_t *ref, uint32_t is_self, asg64_v *b)
void ctg_trans_gp_chain(uint32_t qid, kv_ul_ov_t *res, const ul_idx_t *uref, const ug_opt_t *uopt, int64_t bw, double diff_ec_ul, int64_t qlen, Chain_Data* dp, ma_ug_t *ref, uint32_t is_self, asg64_v *b, double unmatch_max)
{
uint64_t k, l, m = 0, rn = res->n; ul_ov_t rr; uint32_t avid = ((is_self)?(qid):((uint32_t)-1));
for (k = 0; k < rn; k++) {
@@ -17170,7 +17176,7 @@ void ctg_trans_gp_chain(uint32_t qid, kv_ul_ov_t *res, const ul_idx_t *uref, con
for (k = 1, l = 0, b->n = 0; k <= rn; k++) {
if((k == rn) || ((res->a[l].tn>>1) != (res->a[k].tn>>1))) {
// fprintf(stderr, "+[M::%s]\tutg%.6ul\n", __func__, (res->a[l].tn>>1) + 1);
if(((res->a[l].tn>>1) != avid) && (linear_ctg_trans_chain_dp(qid, res->a+l, k-l, uref, uopt, bw, diff_ec_ul, /**0.333333**/0.4, /**0.333333**/0.666666, qlen, ref->u.a[(res->a[l].tn>>1)].len, UG_SKIP_N, UG_ITER_N, UG_DIS_N, dp, &rr, b))) {
if(((res->a[l].tn>>1) != avid) && (linear_ctg_trans_chain_dp(qid, res->a+l, k-l, uref, uopt, bw, diff_ec_ul, /**0.333333**/0.4, unmatch_max, qlen, ref->u.a[(res->a[l].tn>>1)].len, UG_SKIP_N, UG_ITER_N, UG_DIS_N, dp, &rr, b))) {
res->a[m++] = rr;
// fprintf(stderr, "-[M::%s]\tutg%.6ul\n", __func__, rr.tn + 1);
}
@@ -17345,18 +17351,18 @@ void push_ctg_trans_res(uint32_t id, kv_ul_ov_t *in, kv_ul_ov_t *ou)
}
uint32_t direct_ctg_trans_chain(mg_tbuf_t *b, uint32_t id, glchain_t *ll, gdpchain_t *gdp, st_mt_t *sps, haplotype_evdience_alloc *hap, const ul_idx_t *uref, const ug_opt_t *uopt,
int64_t bw, double diff_ec_ul, int64_t max_skip, int64_t ulid, Chain_Data* dp, ma_ug_t *qry, scaf_res_t *qry_sc, ma_ug_t *ref, scaf_res_t *ref_sc, ma_ug_t *gfa, bubble_type *bub, kv_u_trans_t *ta, const asg_t *rg, uint64_t soff)
int64_t bw, double diff_ec_ul, int64_t max_skip, int64_t ulid, Chain_Data* dp, ma_ug_t *qry, scaf_res_t *qry_sc, ma_ug_t *ref, scaf_res_t *ref_sc, ma_ug_t *gfa, bubble_type *bub, kv_u_trans_t *ta, const asg_t *rg, uint64_t soff, uint64_t is_exact)
{
// res->bb.n = 0;
// if(ulid != 86660) return 0;
kv_ul_ov_t *idx = &(ll->lo), *init = &(ll->tk); ///int64_t max_idx;
asg64_v b0, b1; uint32_t is_self = (qry?0:1); idx->n = 0;
cl_trans_gen(id, qry?qry->u.a[id].len:ref->u.a[id].len, qry_sc?&(qry_sc->a[id]):&(ref_sc->a[id]), idx, uref, ref, ref_sc, gfa, bub, ta, is_self);
cl_trans_gen(id, qry?qry->u.a[id].len:ref->u.a[id].len, qry_sc?&(qry_sc->a[id]):&(ref_sc->a[id]), idx, uref, ref, ref_sc, gfa, bub, ta, is_self, is_exact);
if(idx->n == 0) return 0;
copy_asg_arr(b0, (*sps));
ctg_trans_gp_chain(id, idx, uref, uopt, bw, diff_ec_ul, qry?qry->u.a[id].len:ref->u.a[id].len, dp, ref, is_self, &b0);
ctg_trans_gp_chain(id, idx, uref, uopt, bw, diff_ec_ul, qry?qry->u.a[id].len:ref->u.a[id].len, dp, ref, is_self, &b0, ((is_exact)?(0.5):(0.666666)));
copy_asg_arr((*sps), b0);
if(idx->n == 0) return 0;
@@ -17471,7 +17477,7 @@ static void worker_for_ctg_trans_alignment(void *data, long i, int tid)
s->hab[tid]->num_read_base++;
s->hab[tid]->num_correct_base += direct_ctg_trans_chain(s->buf[tid], i, &(s->ll[tid]), &(s->gdp[tid]), &(s->sps[tid]), &(s->hab[tid]->hap), s->uu, s->uopt, G_CHAIN_BW, s->opt->diff_ec_ul, UG_SKIP, i, &(s->hab[tid]->clist.chainDP),
c->qry, c->qry_sc, c->ref, c->ref_sc, c->gfa, c->bub, c->ta, s->rg, c->soff);
c->qry, c->qry_sc, c->ref, c->ref_sc, c->gfa, c->bub, c->ta, s->rg, c->soff, c->is_exact);
}
void rm_dup_aln(u_trans_t *u, uint64_t u_n, asg64_v *b, double dup_cut)
@@ -18974,7 +18980,7 @@ void work_ctg_path_trans(uldat_t *sl, asg_t *sg, ma_ug_t *qry, scaf_res_t *qry_s
fprintf(stderr, "[M::%s::] # try:%d, # done:%d\n", __func__, s.sum_len, s.n);
}
void work_ctg_path_trans_self(uldat_t *sl, asg_t *sg, ma_ug_t *db, scaf_res_t *db_sc, ma_ug_t *gfa, kv_u_trans_t *ta, uint64_t soff, bubble_type *bu, kv_u_trans_t *res)
void work_ctg_path_trans_self(uldat_t *sl, asg_t *sg, ma_ug_t *db, scaf_res_t *db_sc, ma_ug_t *gfa, kv_u_trans_t *ta, uint64_t soff, uint64_t is_exact, bubble_type *bu, kv_u_trans_t *res)
{
utepdat_t s; uint64_t i; memset(&s, 0, sizeof(s));
s.id = 0; s.opt = sl->opt; s.ug = sl->ug; s.uopt = sl->uopt; s.rg = sl->rg; s.uu = sl->uu;
@@ -18985,7 +18991,7 @@ void work_ctg_path_trans_self(uldat_t *sl, asg_t *sg, ma_ug_t *db, scaf_res_t *d
s.hab[i] = ha_ovec_init(0, 0, 1); s.buf[i] = mg_tbuf_init();
}
ctdat_t c; memset(&c, 0, sizeof(c)); c.soff = soff; c.bub = bu;
ctdat_t c; memset(&c, 0, sizeof(c)); c.soff = soff; c.bub = bu; c.is_exact = is_exact;
c.s = &(s); c.qry = NULL; c.qry_sc = NULL; c.ref = db; c.ref_sc = db_sc; c.gfa = gfa; c.ta = ta;
// detect_outlier_len("+++work_ul_gchains");
@@ -19004,7 +19010,6 @@ void work_ctg_path_trans_self(uldat_t *sl, asg_t *sg, ma_ug_t *db, scaf_res_t *d
fprintf(stderr, "[M::%s::] # try:%d, # done:%d\n", __func__, s.sum_len, s.n);
}
uint64_t work_ul_gchains_consensus(uldat_t *sl)
{
utepdat_t s; uint64_t i; memset(&s, 0, sizeof(s));
@@ -21933,17 +21938,18 @@ void gen_contig_trans(const ug_opt_t *uopt, asg_t *sg, ma_ug_t *qry, scaf_res_t
destroy_ul_idx_t(uu);
}
void gen_contig_self(const ug_opt_t *uopt, asg_t *sg, ma_ug_t *db, scaf_res_t *db_sc, ma_ug_t *gfa, kv_u_trans_t *ta, uint64_t soff, bubble_type *bu, kv_u_trans_t *res)
void gen_contig_self(const ug_opt_t *uopt, asg_t *sg, ma_ug_t *db, scaf_res_t *db_sc, ma_ug_t *gfa, kv_u_trans_t *ta, uint64_t soff, bubble_type *bu, kv_u_trans_t *res, uint32_t is_exact)
{
mg_idxopt_t opt; uldat_t sl; int32_t cutoff;
init_aux_table(); ha_opt_update_cov(&asm_opt, asm_opt.hom_cov);
cutoff = asm_opt.max_n_chain;
init_mg_opt(&opt, !(asm_opt.flag&HA_F_NO_HPC), 19, 10, cutoff, asm_opt.max_n_chain, asm_opt.ul_error_rate, asm_opt.ul_error_rate, asm_opt.ul_error_rate_low, asm_opt.ul_error_rate_hpc, asm_opt.ul_ec_round);
init_mg_opt(&opt, !(asm_opt.flag&HA_F_NO_HPC), 19, 10, cutoff, asm_opt.max_n_chain, asm_opt.ul_error_rate, ((is_exact)?(0.333333):(asm_opt.ul_error_rate)), asm_opt.ul_error_rate_low, asm_opt.ul_error_rate_hpc, asm_opt.ul_ec_round);
ul_idx_t *uu = gen_ul_idx_t_sc(db, sg, db_sc, gfa->u.n);
init_uldat_t(&sl, NULL, NULL, &opt, CHUNK_SIZE, asm_opt.thread_num, uopt, uu); sl.rg = sg; sl.ug = db;
work_ctg_path_trans_self(&sl, sg, db, db_sc, gfa, ta, soff, bu, res); uu->ug = NULL;
destroy_ul_idx_t(uu);
work_ctg_path_trans_self(&sl, sg, db, db_sc, gfa, ta, soff, is_exact, bu, res);
uu->ug = NULL; destroy_ul_idx_t(uu);
}
void order_contig_trans(kv_u_trans_t *in)