xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-24 00:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #356 from chhylp123/hifiasm_dev_debug

Browse Source 
Hifiasm dev debug
This commit is contained in:
chhylp123
2022-11-25 20:51:04 -05:00
committed by GitHub
parent deb31948e1 9a454576e1
commit 25dcaaabec
3 changed files with 22 additions and 21 deletions
Download Patch File Download Diff File Expand all files Collapse all files
CommandLines.h
+1 -1
View File
@@ -4,7 +4,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.17.5-r458"
#define HA_VERSION "0.17.6-r460"
#define VERBOSE 0
Correct.cpp
+20 -15
View File
@@ -14762,7 +14762,7 @@ char* qstr, UC_Read *tu, int64_t id, int64_t rev)
return 1;
}
int64_t gen_single_khit(Candidates_list *cl, int64_t ch_n, int64_t h_khit, int64_t mode, int64_t qs, int64_t qe, int64_t ts, int64_t te, int64_t max_skip, int64_t max_iter)
int64_t gen_single_khit(Candidates_list *cl, int64_t ch_n, int64_t h_khit, int64_t mode, int64_t qs, int64_t qe, int64_t ts, int64_t te, int64_t max_skip, int64_t max_iter, int64_t rid)
{
// if(ch_n != 3 || mode != 0 || qs != 171728 || qe != 172258) return 0;
k_mer_hit *ch_a = cl->list + cl->length; int64_t k, i, j, occ, m, ncn, prefix, suffix, srt = 1;
@@ -14770,8 +14770,8 @@ int64_t gen_single_khit(Candidates_list *cl, int64_t ch_n, int64_t h_khit, int64
if(mode == 0 || mode == 2) suffix = 1;
if(mode == 0 || mode == 1) prefix = 1;
// if(ch_n == 2 && mode == 2 && qe - qs == 2419 && te - ts == 2419) {
// fprintf(stderr, "[M::%s::mode->%ld] ch_n::%ld, q::[%ld, %ld), t::[%ld, %ld)\n",
// __func__, mode, ch_n, qs, qe, ts, te);
// fprintf(stderr, "[M::%s::mode->%ld] ch_n::%ld, q::[%ld, %ld), t::[%ld, %ld)\n",
// __func__, mode, ch_n, qs, qe, ts, te);
// }
for (k = occ = m = 0; k < ch_n; k++) {
@@ -14788,13 +14788,14 @@ int64_t gen_single_khit(Candidates_list *cl, int64_t ch_n, int64_t h_khit, int64
ch_n = m; if(!ch_n) return ch_n;
occ += prefix + suffix;
// if(ch_n == 2 && mode == 2 && qe - qs == 2419 && te - ts == 2419) {
// fprintf(stderr, "+[M::%s::] occ::%ld\n", __func__, occ);
// fprintf(stderr, "+[M::%s::] occ::%ld\n", __func__, occ);
// }
ncn = occ + cl->length;
if(cl->size < ncn) {
cl->size = ncn;
cl->list = (k_mer_hit*)realloc(cl->list, (sizeof((*(cl->list)))*cl->length));
REALLOC(cl->list, cl->size);
// cl->list = (k_mer_hit*)realloc(cl->list, (sizeof((*(cl->list)))*cl->length));
}
ch_a = cl->list + cl->length; assert((cl->length+occ)<= cl->size);
@@ -14846,7 +14847,11 @@ int64_t gen_single_khit(Candidates_list *cl, int64_t ch_n, int64_t h_khit, int64
// cht.self_offset, cht.offset, cht.cnt, cht.readID);
}
// if(ch_n == 2 && mode == 2 && qe - qs == 2419 && te - ts == 2419) {
// fprintf(stderr, "-[M::%s::] occ::%ld\n", __func__, occ);
// fprintf(stderr, "-[M::%s::] occ::%ld\n", __func__, occ);
// }
// if(!(occ == 0)) {
// fprintf(stderr, "[M::%s] rid::%ld, name::%.*s\n", __func__, rid,
// (int32_t)UL_INF.nid.a[rid].n, UL_INF.nid.a[rid].a);
// }
assert(occ == 0);
ch_n = occ = ncn - cl->length;
@@ -14906,7 +14911,7 @@ int64_t gen_single_khit(Candidates_list *cl, int64_t ch_n, int64_t h_khit, int64
///[qs, qe) && [ts, te)
int64_t gen_win_chain(overlap_region *z, Candidates_list *cl, int64_t qs, int64_t qe, int64_t ts, int64_t te,
int64_t wl, const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref, char* qstr, UC_Read *tu, bit_extz_t *exz,
int64_t ql, int64_t tl, double e_rate, int64_t h_khit, int64_t mode)
int64_t ql, int64_t tl, double e_rate, int64_t h_khit, int64_t mode, int64_t rid)
{
assert(mode < 3);
int64_t k, ws, we, os, oe, wsk, rcn = cl->length, ncn, occ = 0, ovlp, wn = z->w_list.n; asg16_v ez; uint32_t w = 1;
@@ -14950,15 +14955,15 @@ int64_t ql, int64_t tl, double e_rate, int64_t h_khit, int64_t mode)
// }
ch_n = lchain_qdp_fix(ch_a, ch_n0, &(cl->chainDP), max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip,
e_rate, ql, tl, 1, ((mode==0)||(mode==1))?1:0, ((mode==0)||(mode==2))?1:0);
// fprintf(stderr, "\n[M::%s::] ch_n0::%ld, ch_n::%ld, mode::%ld, ql::%ld, tl::%ld\n",
// __func__, ch_n0, ch_n, mode, qe-qs, te-ts);
for (k = occ = 0; k < ch_n; k++) {
ch_a[k] = ch_a[cl->chainDP.tmp[k]];
if((ch_a[k].cnt&(0xffu))) occ++;
// assert(debug_k_mer_hit_retrive(&(ch_a[k]), hpc_g, rref, uref, qstr, tu, z->y_id, z->y_pos_strand));
}
// fprintf(stderr, "[M::%s::] ch_n0::%ld, ch_n::%ld, mode::%ld, ql::%ld, tl::%ld, occ::%ld\n",
// __func__, ch_n0, ch_n, mode, qe-qs, te-ts, occ);
if(occ <= 0) return 0;
ch_n = gen_single_khit(cl, ch_n, h_khit, mode, qs, qe, ts, te, max_skip, max_iter);
ch_n = gen_single_khit(cl, ch_n, h_khit, mode, qs, qe, ts, te, max_skip, max_iter, rid);
return ch_n;
}
@@ -14974,7 +14979,7 @@ int64_t ql, int64_t tl, int64_t h_khit, int64_t rid)
ts = aux_o->w_list.a[aux_i].y_start; te = aux_o->w_list.a[aux_i].y_end+1;
if(qe - qs < FORCE_SIN_L || te - ts < FORCE_SIN_L) return;
mode = aux_o->w_list.a[aux_i].error_threshold;
ch_n = gen_win_chain(z, cl, qs, qe, ts, te, wl, uref, hpc_g, rref, qstr, tu, exz, ql, tl, e_rate, h_khit, mode);
ch_n = gen_win_chain(z, cl, qs, qe, ts, te, wl, uref, hpc_g, rref, qstr, tu, exz, ql, tl, e_rate, h_khit, mode, rid);
ch_a = cl->list + rcn;
if(ch_n) {
idx.ts = idx.te = (uint32_t)-1; idx.qs = 0; idx.qe = ql; todo = 1;
@@ -15224,7 +15229,7 @@ UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql,
else tl = Get_READ_LENGTH((*rref), id);
for (i = ch_idx; i < cl->length && cl->list[i].readID == cl->list[ch_idx].readID; i++); ch_n = i-ch_idx;
// fprintf(stderr, "\n[M::%s::rid->%ld] utg%.6dl(%c), z::[%u, %u)\n",
// fprintf(stderr, "[M::%s::rid->%ld] utg%.6dl(%c), z::[%u, %u)\n",
// __func__, rid, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], z->x_pos_s, z->x_pos_e+1);
on = fusion_chain_ovlp(z, ch_a, ch_n, ov, on, wl, ql, tl);
aux_o->w_list.n = aux_o->w_list.c.n = 0;
@@ -15234,7 +15239,7 @@ UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql,
for (i = 0; i < on; i++) {
// fprintf(stderr, "[M::%s::i->%ld] ovq::[%u, %u), ovt::[%u, %u), hits::[%d, %d)\n", __func__, i,
// fprintf(stderr, "[M::%s::+i->%ld] ovq::[%u, %u), ovt::[%u, %u), hits::[%d, %d)\n", __func__, i,
// ov->qs, ov->qe, ov->ts, ov->te,
// (ov->qn!=((uint32_t)-1))?(int32_t)ov->qn:-1, (int32_t)ov->tn);
assert((i<=0)||(ov[i].qs>ov[i-1].qe));
@@ -15245,7 +15250,7 @@ UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql,
for (i = 0; i < aux_n; i++) {
if(!(is_ualn_win(aux_o->w_list.a[i]))) continue;
// if((aux_o->w_list.a[i].x_end+1-aux_o->w_list.a[i].x_start) <= FORCE_CNS_L) {
// fprintf(stderr, "[aln::i->%ld::ql->%d] q::[%d, %d), t::[%d, %d), err::%d, clen::%u, mode::%d\n", i,
// fprintf(stderr, "[aln::-i->%ld::ql->%d] q::[%d, %d), t::[%d, %d), err::%d, clen::%u, mode::%d\n", i,
// aux_o->w_list.a[i].x_end+1-aux_o->w_list.a[i].x_start,
// aux_o->w_list.a[i].x_start, aux_o->w_list.a[i].x_end+1,
// aux_o->w_list.a[i].y_start, aux_o->w_list.a[i].y_end+1,
@@ -18917,7 +18922,7 @@ void ul_rid_lalign_adv(overlap_region_alloc* ol, Candidates_list *cl, const ul_i
} else {
for (i = cln->n = trace->n = 0; i < ol->length; i++) {
z = &(ol->list[i]); z->shared_seed = z->non_homopolymer_errors;///for index
// fprintf(stderr, "[M::%s::utg%.6dl(%c)] i::%ld, aln_l::%u, q::[%u, %u), ql::%u\n", __func__,
// fprintf(stderr, "\n[M::%s::utg%.6dl(%c)] i::%lu, aln_l::%u, q::[%u, %u), ql::%u\n", __func__,
// (int32_t)z->y_id + 1, "+-"[z->y_pos_strand], i, z->align_length,
// z->x_pos_s, z->x_pos_e+1, z->x_pos_e+1-z->x_pos_s);
ul_local_aln(z, cl, uref, qu->seq, tu, exz, err, w.window_length, 1000,
inter.cpp
+1 -5
View File
@@ -8927,7 +8927,7 @@ static void worker_for_ul_scall_alignment(void *data, long i, int tid) // callba
uint32_t high_occ = 2; overlap_region *aux_o = NULL;
// if(s->id+i != 901) return;
// if(s->id+i != 1052) return;
// fprintf(stderr, "[0M::%s] rid::%ld, len::%lu, name::%.*s\n", __func__, s->id+i, s->len[i],
// fprintf(stderr, "[M::%s] rid::%ld, len::%lu, name::%.*s\n", __func__, s->id+i, s->len[i],
// (int32_t)UL_INF.nid.a[s->id+i].n, UL_INF.nid.a[s->id+i].a);
// if (memcmp(UL_INF.nid.a[s->id+i].a, "d0aab024-b3a7-40fb-83cc-22c3d6d951f8", UL_INF.nid.a[s->id+i].n-1)) return;
// fprintf(stderr, "[M::%s::] ==> len: %lu\n", __func__, s->len[i]);
@@ -8938,10 +8938,6 @@ static void worker_for_ul_scall_alignment(void *data, long i, int tid) // callba
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
// void ul_rid_lalign_adv(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *uref, const ug_opt_t *uopt,
// char *qstr, uint64_t ql, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate,
// int64_t wl, kv_ul_ov_t *aln, int64_t sid, uint64_t khit, void *km)
ul_rid_lalign_adv(&b->olist, &b->clist, s->uu, s->uopt, s->seq[i], s->len[i], &b->self_read, &b->ovlp_read,
&b->exz, NULL, s->opt->diff_ec_ul, winLen, NULL, NULL, NULL, s->id+i, s->opt->k, NULL);