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has bug multiple threads

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chhylp123
2021-12-28 21:48:41 -05:00
parent 8a0ec3d575
commit dbc72b8c2d
5 changed files with 447 additions and 160 deletions
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inter.cpp
+29 -28
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@@ -288,10 +288,10 @@ typedef struct { // data structure for each step in kt_pipeline()
int n, m, sum_len;
uint64_t *len, id;
char **seq;
ha_mzl_v *mzs;
st_mt_t *sps;
mg_gchains_t **gcs;
mg_tbuf_t **buf;
ha_mzl_v *mzs;///useless
st_mt_t *sps;///useless
mg_gchains_t **gcs;///useless
mg_tbuf_t **buf;///useless
ha_ovec_buf_t **hab;
} utepdat_t;
@@ -2320,6 +2320,7 @@ static void *worker_ul_scall_pipeline(void *data, int step, void *in) // callbac
}
**/
for (i = 0; i < p->n_thread; ++i) ha_ovec_destroy(s->hab[i]);
free(s->hab);
// free(s->buf); free(s->mzs); free(s->sps);
return s;
}
@@ -2337,13 +2338,14 @@ static void *worker_ul_scall_pipeline(void *data, int step, void *in) // callbac
**/
rid = s->id + i;
append_ul_t(&UL_INF, &rid, NULL, 0, s->seq[i], s->len[i], NULL, 0);
// fprintf(stderr, "%.*s\n", (int)s->len[i], s->seq[i]);
free(s->seq[i]); p->total_base += s->len[i];
}
///debug
/**
free(s->gcs);
**/
free(s);
free(s->len); free(s->seq); free(s);
}
return 0;
}
@@ -2380,7 +2382,7 @@ int print_ul_rs(all_ul_t *U_INF)
init_UC_Read(&ur);
for (i = 0; i < U_INF->n; i++) {
p = &(U_INF->a[i]);
retrieve_ul_t(&ur, U_INF, i, 0);
retrieve_ul_t(&ur, NULL, U_INF, i, 0, 0, -1);
fprintf(stderr, ">%s\n", p->n_n);
fprintf(stderr, "%.*s\n", (int)ur.length, ur.seq);
}
@@ -2870,19 +2872,19 @@ void ul_resolve(ma_ug_t *ug, const asg_t *rg, const ug_opt_t *uopt, int hap_n)
uidx_destory();
}
int ul_v_call(mg_idxopt_t *opt, const ug_opt_t *uopt, const asg_t *rg, const enzyme *fn, void *ha_flt_tab, ha_pt_t *ha_idx, ma_ug_t *ug)
int ul_v_call(mg_idxopt_t *opt, const ug_opt_t *uopt, const enzyme *fn, void *ha_flt_tab, ha_pt_t *ha_idx, ma_ug_t *ug)
{
uldat_t sl; memset(&sl, 0, sizeof(sl));
sl.ha_flt_tab = ha_flt_tab;
sl.ha_idx = ha_idx;
sl.opt = opt;
sl.chunk_size = 500000000;
sl.chunk_size = 100000000;
sl.n_thread = asm_opt.thread_num;
sl.ug = ug;
sl.rg = rg;
sl.uopt = uopt;
scall_ul_pipeline(&sl, fn);
print_ul_rs(&UL_INF);
// print_ul_rs(&UL_INF);
debug_retrieve_rc_sub(&UL_INF, &R_INF, &(ug->u), 100);
// if(!load_ul_hits(&sl.hits, &sl.nn, asm_opt.output_file_name)) {
// scall_ul_pipeline(&sl, fn);
// write_ul_hits(&sl.hits, &sl.nn, asm_opt.output_file_name);
@@ -2891,13 +2893,13 @@ int ul_v_call(mg_idxopt_t *opt, const ug_opt_t *uopt, const asg_t *rg, const enz
return 1;
}
ma_ug_t *dedup_HiFis(ma_hit_t_alloc* src, int64_t min_ovlp, int64_t max_hang, uint64_t n_read, int64_t readLen)
ma_ug_t *dedup_HiFis(ma_hit_t_alloc* src, int64_t min_ovlp, int64_t max_hang, int64_t gap_fuzz)
{
uint64_t i, k, qn, tn;
uint64_t i, k, qn, tn, n_read = R_INF.total_reads;
int32_t r; asg_arc_t t, *p = NULL;
asg_t *rg = asg_init();
rg->m_seq = n_read; MALLOC(rg->seq, rg->m_seq);
rg->m_seq = rg->n_seq = n_read; MALLOC(rg->seq, rg->m_seq);
for (i = 0; i < n_read; ++i) rg->seq[i].len = Get_READ_LENGTH(R_INF, i);
for (i = 0; i < n_read; i++) {
@@ -2906,6 +2908,8 @@ ma_ug_t *dedup_HiFis(ma_hit_t_alloc* src, int64_t min_ovlp, int64_t max_hang, ui
if(!src[i].buffer[k].el) continue;
qn = Get_qn(src[i].buffer[k]); tn = Get_tn(src[i].buffer[k]);
if(rg->seq[qn].del || rg->seq[tn].del) continue;
if((Get_qe(src[i].buffer[k]) - Get_qs(src[i].buffer[k])) < min_ovlp) continue;
if((Get_te(src[i].buffer[k]) - Get_ts(src[i].buffer[k])) < min_ovlp) continue;
r = ma_hit2arc(&(src[i].buffer[k]), rg->seq[qn].len, rg->seq[tn].len, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
if (r == MA_HT_QCONT) {
rg->seq[qn].del = 1;
@@ -2922,6 +2926,8 @@ ma_ug_t *dedup_HiFis(ma_hit_t_alloc* src, int64_t min_ovlp, int64_t max_hang, ui
if(!src[i].buffer[k].el) continue;
qn = Get_qn(src[i].buffer[k]); tn = Get_tn(src[i].buffer[k]);
if(rg->seq[qn].del || rg->seq[tn].del) continue;
if((Get_qe(src[i].buffer[k]) - Get_qs(src[i].buffer[k])) < min_ovlp) continue;
if((Get_te(src[i].buffer[k]) - Get_ts(src[i].buffer[k])) < min_ovlp) continue;
r = ma_hit2arc(&(src[i].buffer[k]), rg->seq[qn].len, rg->seq[tn].len, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
if (r >= 0) {
p = asg_arc_pushp(rg);
@@ -2931,34 +2937,29 @@ ma_ug_t *dedup_HiFis(ma_hit_t_alloc* src, int64_t min_ovlp, int64_t max_hang, ui
}
asg_cleanup(rg); asg_symm(rg);
asg_arc_del_trans(rg, gap_fuzz);
ma_ug_t *ug = NULL;
ug = ma_ug_gen(rg);
asg_destroy(rg);
asg_destroy(rg); ma_ug_destroy(ug);
for (i = k = 0; i < ug->u.n; i++) k += ug->u.a[i].len;
fprintf(stderr, "[M::%s::] # unitigs: %lu, # bases: %lu\n", __func__, (uint64_t)ug->u.n, k);
return ug;
}
void ul_load(const ug_opt_t *uopt)
{
fprintf(stderr, "[M::%s::] ==> UL\n", __func__);
mg_idxopt_t opt;
ma_ug_t *ug = NULL;
ma_ug_t *ug = dedup_HiFis(uopt->sources, uopt->min_ovlp, uopt->max_hang, uopt->gap_fuzz);
int cutoff = asm_opt.hom_cov * asm_opt.high_factor;
init_aux_table();
init_mg_opt(&opt, !(asm_opt.flag&HA_F_NO_HPC), 19, 10, cutoff);
/**
int exist = (asm_opt.load_index_from_disk? uidx_load(&ha_flt_tab, &ha_idx, asm_opt.output_file_name) : 0);
if(exist == 0) uidx_l_build(ug, &opt, cutoff);
if(exist == 0) uidx_write(ha_flt_tab, ha_idx, asm_opt.output_file_name);
ul_v_call(&opt, uopt, /**rg**/NULL, asm_opt.ar, ha_flt_tab, ha_idx, /**ug**/NULL);
**/
ul_v_call(&opt, uopt, asm_opt.ar, ha_flt_tab, ha_idx, ug);
ma_ug_destroy(ug); destory_all_ul_t(&UL_INF);
}