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disable function for tangles with low-coverage ul

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chhylp123
2023-03-10 15:34:10 -05:00
parent af4be8ca1a
commit 8b79a3f22e
2 changed files with 109 additions and 10 deletions
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CommandLines.h
+1 -1
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@@ -5,7 +5,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.19.0-r550"
#define HA_VERSION "0.19.0-r553"
#define VERBOSE 0
gfa_ut.cpp
+108 -9
View File
@@ -115,6 +115,7 @@ typedef struct {
size_t n, m;
uint32_t id:31, is_del:1;
uint32_t cn;
// uint8_t is_consist;
} ul2ul_item_t;
typedef struct {
@@ -6281,8 +6282,8 @@ void integer_gen_ovlp(ul_resolve_t *uidx, integer_t *buf, uint32_t qid, ul2ul_it
{
ul_str_idx_t *str_idx = &(uidx->pstr); ma_ug_t *ug = uidx->l1_ug; ul2ul_t res;
ul_str_t *str = &(str_idx->str.a[qid]); integer_aln_t *p; ul_chain_t sc;
uint64_t k, z, *hid_a, hid_n, sck, b_n, m; uint32_t vk, vz; uc_block_t *xi;
o->n = o->cn = 0; o->id = qid; o->is_del = 0;
uint64_t k, z, *hid_a, hid_n, sck, b_n, m/**, ovn = 0**/; uint32_t vk, vz; uc_block_t *xi;
o->n = o->cn = 0; o->id = qid; o->is_del = 0; ///o->is_consist = 0;
// if(qid == 95 || qid == 36) print_integer_seq(ug, str_idx->str.a, qid, 1);
if(str->cn < 2) return;
for (k = 0, buf->b.n = 0; k < str->cn; k++) {
@@ -6316,6 +6317,14 @@ void integer_gen_ovlp(ul_resolve_t *uidx, integer_t *buf, uint32_t qid, ul2ul_it
}
radix_sort_integer_aln_t_srt(buf->b.a, buf->b.a + buf->b.n);
// b_n = buf->b.n;
// for (k = 1, z = ovn = 0; k <= b_n; k++) {
// if(k == b_n || (buf->b.a[z].tn_rev_qk>>33) != (buf->b.a[k].tn_rev_qk>>33)) {
// ovn++; z = k;
// }
// }
b_n = buf->b.n; buf->sc.n = 0;
for (k = 1, z = 0; k <= b_n; k++) {
if(k == b_n || (buf->b.a[z].tn_rev_qk>>32) != (buf->b.a[k].tn_rev_qk>>32)) {
@@ -6360,7 +6369,8 @@ void integer_gen_ovlp(ul_resolve_t *uidx, integer_t *buf, uint32_t qid, ul2ul_it
// // v = ((uint32_t)str->a[str->cn-1]);
// // nv = asg_arc_n(g, v); av = asg_arc_a(g, v);
// }
o->cn = o->n;
o->cn = o->n;
// if(ovn == o->cn) o->is_consist = 1;
if(o->n <= 0) return;
}
@@ -6660,6 +6670,32 @@ void gen_integer_normalize(ul_resolve_t *uidx)
}
}
uint64_t dd_path_connect(asg_t *g, ul_str_t *str)
{
if(str->cn < 2) return 1;///actually should return 1, doesn't matter
uint64_t i, v, w, nv, k; asg_arc_t *av;
v = ((uint32_t)str->a[0]);
for (i = 1; i < str->cn; i++) {
w = ((uint32_t)str->a[i]);
nv = asg_arc_n(g, v); av = asg_arc_a(g, v);
for (k = 0; k < nv; k++) {
if(av[k].del) continue;
if(av[k].v == w) break;
}
if(k >= nv) return 0;
nv = asg_arc_n(g, w^1); av = asg_arc_a(g, w^1);
for (k = 0; k < nv; k++) {
if(av[k].del) continue;
if(av[k].v == (v^1)) break;
}
if(k >= nv) return 0;
v = w;
}
return 1;
}
void clip_integer_chimeric(ul_resolve_t *uidx, uint32_t qid, ul2ul_item_t *o, ul2ul_idx_t *ul2, integer_t *buf, int64_t min_dp)
{
@@ -6732,6 +6768,14 @@ void clip_integer_chimeric(ul_resolve_t *uidx, uint32_t qid, ul2ul_item_t *o, ul
if(is_left == 0 && is_right == 0) is_del = 1;
if(is_left && is_right && is_middle) is_del = 1;
}
// if(is_del && str->cn > 1 && o->is_consist && dd_path_connect(uidx->l1_ug->g, str)) {
// is_del = 0;
// }
// fprintf(stderr, "[M::%s] qid::%u, o->is_consist::%u, str->cn::%u, is_connect::%lu\n",
// __func__, qid, o->is_consist, str->cn, dd_path_connect(uidx->l1_ug->g, str));
/**
if(!is_del) {
for (k = 0; k < str->cn; k++) {
@@ -12659,6 +12703,7 @@ typedef struct {
uint64_t int_an;
uint64_t *ridx_a;
uint64_t *ridx;
// uint8_t is_double_check;
} unique_bridge_check_t;
uint64_t get_arc_support(ul_resolve_t *uidx, uint64_t v, uint64_t w)
@@ -12767,6 +12812,53 @@ uint64_t get_arc_support_chain(ul_resolve_t *uidx, uint64_t *a, uint64_t a_n, us
return occ;
}
// uint64_t is_consist_ul(ul_resolve_t *uidx, uint64_t *a, uint64_t a_n, usg_t *ng)
// {
// if(a_n <= 0) return 0;
// uint64_t k, v, w, z, *hid_a, hid_n, ulid, i; ul2ul_item_t *it;;
// ul_str_idx_t *str_idx = &(uidx->pstr);
// for (k = 0; k < a_n; k++) {
// v = (ng->a[a[k]>>1].mm<<1)|(a[k]&1);
// hid_a = str_idx->occ.a + str_idx->idx.a[v>>1];
// hid_n = str_idx->idx.a[(v>>1)+1] - str_idx->idx.a[v>>1];
// for (z = 0; z < hid_n; z++) {
// ulid = hid_a[z]>>32;
// if(ulid < uidx->uovl.uln) {
// it = get_ul_ovlp(&(uidx->uovl), ulid, 1);
// if(!it) continue;
// assert(uidx->pstr.str.a[ulid].cn > 1);
// if(it->is_consist == 0) return 0;
// }
// }
// }
// uint64_t nv; asg_arc_t *av;
// v = (ng->a[a[0]>>1].mm<<1)|(a[0]&1);
// for (i = 1; i < a_n; i++) {
// w = (ng->a[a[i]>>1].mm<<1)|(a[i]&1);
// nv = asg_arc_n(uidx->l1_ug->g, v);
// av = asg_arc_a(uidx->l1_ug->g, v);
// for (k = 0; k < nv; k++) {
// if(av[k].del) continue;
// if(av[k].v == w) break;
// }
// if(k >= nv) return 0;
// nv = asg_arc_n(uidx->l1_ug->g, w^1);
// av = asg_arc_a(uidx->l1_ug->g, w^1);
// for (k = 0; k < nv; k++) {
// if(av[k].del) continue;
// if(av[k].v == (v^1)) break;
// }
// if(k >= nv) return 0;
// v = w;
// }
// return 1;
// }
static void worker_unique_bridge_check_s(void *data, long i, int tid) // callback for kt_for()
{
unique_bridge_check_t *uaux = (unique_bridge_check_t *)data;
@@ -12783,7 +12875,9 @@ static void worker_unique_bridge_check_s(void *data, long i, int tid) // callbac
// (ng->a[integer_seq[k]>>1].mm<<1)|(integer_seq[k]&1));
nse = get_arc_support_chain(uaux->uidx, integer_seq+k-1, 2, ng);
if(nse < unique_bridge_occ) {
gidx[i] |= ((uint64_t)0x8000000000000000); return;
// if((!(uaux->is_double_check)) || (!is_consist_ul(uaux->uidx, integer_seq+k-1, 2, ng))) {
gidx[i] |= ((uint64_t)0x8000000000000000); return;
// }
}
}
if(IF_HOM((integer_seq[k]>>1), *bub)) continue;
@@ -12793,7 +12887,9 @@ static void worker_unique_bridge_check_s(void *data, long i, int tid) // callbac
// nse = get_arc_support(uaux->uidx, v, w);
nse = get_arc_support_chain(uaux->uidx, integer_seq+vk, wk+1-vk, ng);
if(nse < unique_bridge_occ) {
gidx[i] |= ((uint64_t)0x8000000000000000); return;
// if((!(uaux->is_double_check)) || (!is_consist_ul(uaux->uidx, integer_seq+vk, wk+1-vk, ng))) {
gidx[i] |= ((uint64_t)0x8000000000000000); return;
// }
}
}
vk = wk;
@@ -12808,6 +12904,10 @@ uint32_t ava_pass_unique_bridge_cov(ul_resolve_t *uidx, usg_t *g, asg64_v *b64,
uaux.uidx = uidx; uaux.integer_seq = integer_seq;
uaux.gidx = b64->a + g_s; uaux.gidx_n = g_e - g_s;
uaux.interval_idx = b64->a; uaux.ng = g;
///if tip_l == 0, it is more likely to be right, so give more chance by double checking
// if(!tip_l) uaux.is_double_check = 1;
// else uaux.is_double_check = 0;
kt_for(uidx->str_b.n_thread, worker_unique_bridge_check_s, (&uaux), g_e-g_s);///seq->n > 1
for (i = g_s; i < g_e; i++) {///available intervals within the same cluster
@@ -12849,8 +12949,7 @@ uint8_t *ff, uint32_t *ng_occ, uint32_t max_ext)
if(k == b64->n || (b64->a[k]>>32) != (b64->a[i]>>32)) {
tip_l = ava_pass_unique_bridge_tips(ng, b64, i, k, int_a, ff, max_ext);
if(tip_l < max_ext) {///no long tip
if(ava_pass_unique_bridge_cov(uidx, ng, b64, i, k, int_a, tip_l))
{
if(/**(!tip_l) || (**/ava_pass_unique_bridge_cov(uidx, ng, b64, i, k, int_a, tip_l)) {
for (z = i; z < k; z++) {
b64->a[mm++] = b64->a[z];
}
@@ -15730,11 +15829,11 @@ void u2g_threading(ul_resolve_t *uidx, ulg_opt_t *ulopt, uint64_t cov_cutoff, ui
for (z = 0; z < ub->n; z++) {///all unreliable arcs
i = ub->a[z]; tm = 1; p = get_usg_arc(ng, seq->a[i].v, seq->a[i+1].v);
if(p) {
if(p->ou < (uint64_t)tm) p->ou = tm;
if(p->ou < (uint64_t)tm) p->ou = tm;///since the initial ou is 0, p->ou = 1
pushp_usg_arc_mm(ng, seq->a[i].v, seq->a[i+1].v, k, i);
p = get_usg_arc(ng, seq->a[i+1].v^1, seq->a[i].v^1);
if(p->ou < (uint64_t)tm) p->ou = tm;
if(p->ou < (uint64_t)tm) p->ou = tm;///since the initial ou is 0, p->ou = 1
pushp_usg_arc_mm(ng, seq->a[i+1].v^1, seq->a[i].v^1, k, i);
}
///give up unreliable arcs if they are not adjacent