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update for reference read hpc

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chhylp123
2024-10-27 13:22:06 -04:00
parent fc98214321
commit ade800990e
6 changed files with 201 additions and 36 deletions
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ecovlp.cpp
+29 -10
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@@ -2865,6 +2865,23 @@ void prt_ovlp_sam(overlap_region_alloc* ol, UC_Read* tu, char *ref_seq, int32_t
fclose(fp);
}
void stderr_phase_ovlp(overlap_region_alloc* ol)
{
int64_t on = ol->length, k; overlap_region *z;
if(!on) return;
uint64_t qry_n = 0, rid, ref_n, qid;
rid = ol->list[0].x_id; ref_n = Get_NAME_LENGTH(R_INF, rid);
for (k = 0; k < on; k++) {
z = &(ol->list[k]); qid = ol->list[k].y_id;
qry_n = Get_NAME_LENGTH(R_INF, qid);
fprintf(stderr, "%.*s(qid::%lu)\tql::%lu\tq::[%u,\t%u)\t%c\t%.*s(tid::%lu)\ttl::%lu\tt::[%u,\t%u)\ttrans::%u\n",
(int32_t)Get_NAME_LENGTH(R_INF, rid), Get_NAME(R_INF, rid), rid, ref_n, z->x_pos_s, z->x_pos_e + 1, "+-"[z->y_pos_strand],
(int32_t)Get_NAME_LENGTH(R_INF, qid), Get_NAME(R_INF, qid), qid, qry_n, z->y_pos_s, z->y_pos_e + 1, ((z->is_match==1)?(0):(1)));
}
}
void dedup_chains(overlap_region_alloc* ol)
{
uint64_t k, l, s, m, mm_k, mm_m, sf; int64_t sc, mm_sc, plus, minus; overlap_region *z, t;
@@ -2931,11 +2948,11 @@ static void worker_hap_ec(void *data, long i, int tid)
**/
// if(i < 1100000 || i > 1400000) return;
// if(i % 100000 == 0) fprintf(stderr, "-a-[M::%s-beg] rid->%ld\n", __func__, i);
// if (memcmp("m64062_190807_194840/180552420/ccs"/**"m64062_190803_042216/161743554/ccs"**//**"m64062_190806_063919/15403289/ccs"**/, Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
// fprintf(stderr, "-a-[M::%s-beg] rid->%ld\n", __func__, i);
// } else {
// return;
// }
if (memcmp("4da034b0-a94d-4576-8481-c0d9a9f96d40", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
fprintf(stderr, "-a-[M::%s-beg] rid->%ld\n", __func__, i);
} else {
return;
}
// if(i != 3028559) return;
// if(i != 306) return;
@@ -2970,10 +2987,12 @@ static void worker_hap_ec(void *data, long i, int tid)
// b->num_correct_base += b->olist.length;
copy_asg_arr(buf0, b->sp);
rphase_hc(&b->olist, &R_INF, &b->hap, &b->self_read, &b->ovlp_read, &b->pidx, &b->v64, &buf0, 0, WINDOW_MAX_SIZE, b->self_read.length, 1/**, 0**/, i);
copy_asg_arr(buf0, b->sp);
rphase_hc(&b->olist, &R_INF, &b->hap, &b->self_read, &b->ovlp_read, &b->pidx, &b->v64, &buf0, 0, WINDOW_MAX_SIZE, b->self_read.length, 1/**, 0**/, i, (asm_opt.is_ont)?HPC_PL:0);
copy_asg_arr(b->sp, buf0);
// stderr_phase_ovlp(&b->olist);
dedup_chains(&b->olist);
copy_asg_arr(buf0, b->sp);
@@ -4999,9 +5018,9 @@ static void worker_hap_dc_ec0(void *data, long i, int tid)
b->cnt[0] += b->self_read.length;
copy_asg_arr(buf0, b->sp);
rphase_hc(&b->olist, &R_INF, &b->hap, &b->self_read, &b->ovlp_read, &b->pidx, &b->v64, &buf0, 0, WINDOW_MAX_SIZE, b->self_read.length, 1/**, 1**/, i);
copy_asg_arr(b->sp, buf0);
copy_asg_arr(buf0, b->sp);
rphase_hc(&b->olist, &R_INF, &b->hap, &b->self_read, &b->ovlp_read, &b->pidx, &b->v64, &buf0, 0, WINDOW_MAX_SIZE, b->self_read.length, 1/**, 1**/, i, (asm_opt.is_ont)?HPC_PL:0);
copy_asg_arr(b->sp, buf0);
copy_asg_arr(buf0, b->sp);
b->cnt[1] += wcns_gen(&b->olist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, &b->pidx, &b->v64, &buf0, 0, 512, b->self_read.length, 3, 0.500001, aux_o, &b->v32, &b->cns, 256, i);