xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-28 03:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r465

Browse Source
This commit is contained in:
chhylp123
2022-12-02 09:40:25 -05:00
parent a4d6cebc32
commit 786f8bdff0
6 changed files with 967 additions and 27 deletions
Download Patch File Download Diff File Expand all files Collapse all files
hic.cpp
+189 -12
View File
@@ -15,6 +15,7 @@
#include "kseq.h" // FASTA/Q parser
#include "kdq.h"
#include "horder.h"
#include "gfa_ut.h"
KSEQ_INIT(gzFile, gzread)
KDQ_INIT(uint64_t)
@@ -16481,15 +16482,14 @@ void optimize_u_trans(kv_u_trans_t *ovlp, kvec_pe_hit* hits, ha_ug_index* idx)
x = &(ovlp->a[i]);
if(x->qn > x->tn) continue;
if(x->f != RC_2 || x->del) continue;
occ = get_oe_occ(x->qn, x->tn, hits, idx) + get_oe_occ(x->tn, x->qn, hits, idx);
occ = get_oe_occ(x->qn, x->tn, hits, idx) + get_oe_occ(x->tn, x->qn, hits, idx);///how many UL bridging qn and tn
kv_pushp(u_trans_t, k_trans, &p);
(*p) = (*x); p->nw = (x->nw*(1-(((double)(occ<<1))/((double)(hits->occ.a[x->qn]+hits->occ.a[x->tn])))));
if(p->nw < 0) fprintf(stderr, "ERROR-nw\n");
if(p->nw == 0) p->nw = x->nw*0.005;
if(p->nw == 0) {
k_trans.n--;
}
else {
} else {
kv_pushp(u_trans_t, k_trans, &p);
(*p) = k_trans.a[k_trans.n-2];
p->qn = k_trans.a[k_trans.n-2].tn; p->qs = k_trans.a[k_trans.n-2].ts; p->qe = k_trans.a[k_trans.n-2].te;
@@ -16540,6 +16540,179 @@ ha_ug_index* idx, uint64_t step, uint64_t total)
}
void prt_hits_noid(ha_ug_index* idx, ma_ug_t* ug, kvec_pe_hit* hits, FILE *fn)
{
uint64_t k, shif = 64 - idx->uID_bits;
char dir[2] = {'+', '-'};
for (k = 0; k < hits->a.n; ++k) {
fprintf(fn, "r-%lu-th\t%c\trs-utg%.6d%c\t%lu\t%c\tre-utg%.6d%c\t%lu\n",
hits->a.a[k].id,
dir[hits->a.a[k].s>>63], (int)((hits->a.a[k].s<<1)>>shif)+1,
"lc"[ug->u.a[((hits->a.a[k].s<<1)>>shif)].circ], hits->a.a[k].s&idx->pos_mode,
dir[hits->a.a[k].e>>63], (int)((hits->a.a[k].e<<1)>>shif)+1,
"lc"[ug->u.a[((hits->a.a[k].e<<1)>>shif)].circ], hits->a.a[k].e&idx->pos_mode);
}
}
void prt_utg_trans(kv_u_trans_t *ta, ma_ug_t* ug, FILE *fn)
{
uint32_t i;
u_trans_t *p = NULL;
for (i = 0; i < ta->n; i++) {
p = &(ta->a[i]);
fprintf(fn, "utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\tw(%f)\tf(%u)\n",
p->qn+1, "lc"[ug->u.a[p->qn].circ], ug->u.a[p->qn].len, p->qs, p->qe, "+-"[p->rev],
p->tn+1, "lc"[ug->u.a[p->tn].circ], ug->u.a[p->tn].len, p->ts, p->te, p->nw, p->f);
}
}
void prt_kv_u_trans(kv_u_trans_t *ta, hc_links* lk, int8_t *s, FILE *fn)
{
uint32_t i;
u_trans_t *p = NULL;
hc_edge *e = NULL;
for (i = 0; i < ta->n; i++) {
p = &(ta->a[i]);
e = get_hc_edge(lk, p->qn, p->tn, 0);
fprintf(fn, "s-utg%.6ul\tS(%d)\td-utg%.6ul\tS(%d)\trev(%u)\td(%lld)\ttw(%f)\n",
p->qn+1, s[p->qn], p->tn+1, s[p->tn], p->rev,
(e == NULL || e->dis == (uint64_t)-1)? -1 : (long long)(e->dis>>3), p->nw);
}
}
void prt_bubble_gfa_adv(FILE *fp, bubble_type *bub, const char* utg_pre, const char* bub_pre, const char* chain_pre)
{
uint32_t i, k, m, *a, n, beg, sink, x; ma_utg_t *p; uint64_t occ;
ma_ug_t *b_ug = bub->b_ug; char name[32], bname[32]; uint8_t *f; CALLOC(f, bub->ug->u.n);
for (i = 0; i < b_ug->u.n; i++) {
p = &b_ug->u.a[i];
if(p->n == 0) continue;
for (k = occ = 0; k < p->n; k++){
x = p->a[k]>>33;
get_bubbles(bub, x, &beg, &sink, &a, &n, NULL);
for (m = 0; m < n; m++) {
occ += bub->ug->u.a[a[m]>>1].n; f[a[m]>>1] = 1;
}
if(beg != (uint32_t)-1 && f[beg>>1] == 0) {
occ += bub->ug->u.a[beg>>1].n; f[beg>>1] = 1;
}
if(sink != (uint32_t)-1 && f[sink>>1] == 0) {
occ += bub->ug->u.a[sink>>1].n; f[sink>>1] = 1;
}
}
sprintf(name, "%s%.6d%c", chain_pre, i + 1, "lc"[p->circ]);
fprintf(fp, "S\t%s\t*\tLN:i:%lu\n", name, occ);
for (k = 0; k < p->n; k++) {
x = p->a[k]>>33;
sprintf(bname, "%s%.6d", bub_pre, x + 1);
fprintf(fp, "B\t%s\t%c\tcid:i:%s\tsm:%c\n", bname, "+-"[(p->a[k]>>32)&1], name, "01"[x<bub->f_bub]);
get_bubbles(bub, x, &beg, &sink, &a, &n, NULL);
if(beg != (uint32_t)-1) {
fprintf(fp, "U\t%s%.6d%c\t%c\tcid:i:%s\tbid:b:%s\thom:%c\n",
utg_pre, (beg>>1)+1, "lc"[bub->ug->u.a[(beg>>1)].circ], "+-"[beg&1], name, bname, "10"[IF_HOM((beg>>1), *bub)]);
}
if(sink != (uint32_t)-1) {
fprintf(fp, "U\t%s%.6d%c\t%c\tcid:i:%s\tbid:s:%s\thom:%c\n",
utg_pre, (sink>>1)+1, "lc"[bub->ug->u.a[(sink>>1)].circ], "+-"[sink&1], name, bname, "10"[IF_HOM((sink>>1), *bub)]);
}
for (m = 0; m < n; m++) {
occ += bub->ug->u.a[a[m]>>1].n;
fprintf(fp, "U\t%s%.6d%c\t%c\tcid:i:%s\tbid:c:%s\thom:%c\n",
utg_pre, (a[m]>>1)+1, "lc"[bub->ug->u.a[(a[m]>>1)].circ], "+-"[a[m]&1], name, bname, "10"[IF_HOM((a[m]>>1), *bub)]);
}
}
}
asg_arc_t* au = NULL;
uint32_t nu, u, v, j;
for (i = 0; i < b_ug->u.n; ++i) {
if(b_ug->u.a[i].m == 0) continue;
if(b_ug->u.a[i].circ)
{
fprintf(fp, "L\t%s%.6dc\t+\t%s%.6dc\t+\t%dM\tL1:i:%d\n",
chain_pre, i+1, chain_pre, i+1, 0, 0);
fprintf(fp, "L\t%s%.6dc\t-\t%s%.6dc\t-\t%dM\tL1:i:%d\n",
chain_pre, i+1, chain_pre, i+1, 0, 0);
}
u = i<<1;
au = asg_arc_a(b_ug->g, u);
nu = asg_arc_n(b_ug->g, u);
for (j = 0; j < nu; j++)
{
if(au[j].del) continue;
v = au[j].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\n",
chain_pre, (u>>1)+1, "lc"[b_ug->u.a[u>>1].circ], "+-"[u&1],
chain_pre, (v>>1)+1, "lc"[b_ug->u.a[v>>1].circ], "+-"[v&1], 0, 0);
}
u = (i<<1) + 1;
au = asg_arc_a(b_ug->g, u);
nu = asg_arc_n(b_ug->g, u);
for (j = 0; j < nu; j++)
{
if(au[j].del) continue;
v = au[j].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\n",
chain_pre, (u>>1)+1, "lc"[b_ug->u.a[u>>1].circ], "+-"[u&1],
chain_pre, (v>>1)+1, "lc"[b_ug->u.a[v>>1].circ], "+-"[v&1], 0, 0);
}
}
for (i = 0; i < bub->ug->u.n; i++) {
if(f[i]) continue;
fprintf(fp, "U\t%s%.6d%c\t+\tcid:i:*\tbid:c:*\thom:%c\n",
utg_pre, i+1, "lc"[bub->ug->u.a[i].circ], "10"[IF_HOM(i, *bub)]);
}
free(f);
}
void prt_debug_hic(const char* o_n, ma_ug_t* ug, ha_ug_index* idx, ug_opt_t *opt, kvec_pe_hit* hits,
kv_u_trans_t *utg_trans, kv_u_trans_t *p_arcs, hc_links* lk, int8_t *s, bubble_type *bub)
{
char* gfa_name = (char*)malloc(strlen(o_n)+100); FILE *fn = NULL;
sprintf(gfa_name, "%s.hic.dbg", o_n);
print_debug_gfa(idx->read_g, idx->ug, opt->coverage_cut, gfa_name, opt->sources, opt->ruIndex,
opt->max_hang, opt->min_ovlp, 0, 0, 0);
if(hits) {
sprintf(gfa_name, "%s.hic.hits.log", o_n); fn = fopen(gfa_name, "w");
prt_hits_noid(idx, ug, hits, fn);
fclose(fn);
}
if(utg_trans) {
sprintf(gfa_name, "%s.hic.utg.trans.log", o_n); fn = fopen(gfa_name, "w");
prt_utg_trans(utg_trans, ug, fn);
fclose(fn);
}
if(p_arcs) {
sprintf(gfa_name, "%s.hic.parcs.log", o_n); fn = fopen(gfa_name, "w");
prt_kv_u_trans(p_arcs, lk, s, fn);
fclose(fn);
}
if(bub) {
sprintf(gfa_name, "%s.bub.noseq.gfa", o_n); fn = fopen(gfa_name, "w");
prt_bubble_gfa_adv(fn, bub, "utg", "btg", "ctg");
fclose(fn);
}
free(gfa_name);
fprintf(stderr, "[M::%s::] done\n", __func__);
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt, kvec_pe_hit **rhits)
{
double index_time = yak_realtime();
@@ -16608,11 +16781,15 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
// if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s);
// update_trans_g(idx, &k_trans, &bub);
/*******************************for debug************************************/
// mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
// (bub.round_id == 0? 1 : 0), s->s, 1, (asm_opt.ar)?(&bub):(NULL), &(idx->t_ch->k_trans), 0,
// (((bub.round_id+1) == bub.n_round)?1:0));
mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
(bub.round_id == 0? 1 : 0), s->s, 1, NULL, &(idx->t_ch->k_trans), 0, 0);
(bub.round_id == 0? 1 : 0), s->s, 1, &bub,
&(idx->t_ch->k_trans), 0, 0/**(((bub.round_id+1) == bub.n_round)?1:0)**/);
// mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
// (bub.round_id == 0? 1 : 0), s->s, 1, NULL, &(idx->t_ch->k_trans), 0, 0);
// if((bub.round_id+1) == bub.n_round) {
// prt_debug_hic(asm_opt.output_file_name, idx->ug, idx, opt, &sl.hits,
// &(idx->t_ch->k_trans), &k_trans, &link, s->s, &(bub));
// }
/*******************************for debug************************************/
label_unitigs_sm(s->s, NULL, idx->ug);
@@ -16642,15 +16819,15 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
// horder_t *ho = init_horder_t(&sl.hits, idx->uID_bits, idx->pos_mode, idx->read_g, idx->ug, &bub, &(idx->t_ch->k_trans), opt, 3);
///print_hc_links(&link, 0, &hap);
// print_hc_links(&link, 0, &hap);
// print_hits_simp(idx, &sl.hits);
// print_kv_u_trans_t(&(idx->t_ch->k_trans));
// print_kv_u_trans(&k_trans, &link, s->s);
// print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, NULL/**idx->link**/, idx);
// print_hits(idx, &sl.hits, fn1, fn2);
///print_debug_bubble_graph(&bub, idx->ug, asm_opt.output_file_name);
// print_debug_bubble_graph(&bub, idx->ug, asm_opt.output_file_name);
// print_bubble_chain(&bub);
// destory_contig_partition(&hap);
// destory_horder_t(&ho);
kv_destroy(sl.hits.a); kv_destroy(sl.hits.idx); kv_destroy(sl.hits.occ);