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bug fix

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chhylp123
2021-05-02 14:16:36 -04:00
parent 9c205c8271
commit 24e5453781
6 changed files with 90 additions and 29 deletions
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29
Overlaps.cpp
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@@ -11200,7 +11200,7 @@ uint32_t only_len)
break;
}
}
if(k == nv) fprintf(stderr, "ERROR\n");
if(k == nv) fprintf(stderr, "ERROR-set_utg_offset\n");
}
p_v = v; len += l;
@@ -11272,8 +11272,8 @@ void refine_u_trans_t(u_trans_hit_t *q, kv_ca_buf_t* cb)
if(si != cb->n && ei != cb->n) break;
}
if(si == 0 || ei == 0) fprintf(stderr, "ERROR\n");
if(si >= cb->n || ei >= cb->n) fprintf(stderr, "ERROR\n");
if(si == 0 || ei == 0) fprintf(stderr, "ERROR-si-ei-0\n");
if(si >= cb->n || ei >= cb->n) fprintf(stderr, "ERROR-si-ei-1\n");
si--; ei--;
if(s < cb->a[si].c_x_p || ((si + 1) < cb->n && s >= cb->a[si + 1].c_x_p))
@@ -11452,7 +11452,7 @@ uint32_t get_u_trans_hit(u_trans_hit_idx *t, u_trans_hit_t *hit)
break;
}
}
if(k == nv) fprintf(stderr, "ERROR\n");
if(k == nv) fprintf(stderr, "ERROR-nv\n");
}
///[t->cBeg, t->cEnd)
@@ -12762,12 +12762,6 @@ long long gap_fuzz, bub_label_t* b_mask_t)
if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_trans_chain(cov->t_ch, output_file_name);
}
hic_analysis(ug, sg, cov?cov->t_ch:t_ch);
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.clean_d_utg.noseq.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
@@ -12775,9 +12769,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
fclose(output_file);
free(gfa_name);
hic_analysis(ug, sg, cov?cov->t_ch:t_ch);
if(cov) destory_hap_cov_t(&cov);
if(t_ch) destory_trans_chain(&t_ch);
@@ -16593,13 +16585,13 @@ void chain_origin_trans_uid_s_bubble(buf_t *pri, buf_t* aux, uint32_t beg, uint3
for (i = 0; i < nv; ++i)
{
if(av[i].del) continue;
if(av[i].v == pri_v) priEnd = pri_len - av[i].ol - 1;
if(av[i].v == aux_v) auxEnd = aux_len - av[i].ol - 1;
if(av[i].v == pri_v) priEnd = ((pri_len > av[i].ol)? (pri_len - av[i].ol - 1) : 0);
if(av[i].v == aux_v) auxEnd = ((aux_len > av[i].ol)? (aux_len - av[i].ol - 1) : 0);
}
if(priBeg == (uint32_t)-1 || priEnd == (uint32_t)-1 || auxBeg == (uint32_t)-1 || auxEnd == (uint32_t)-1)
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "ERROR-s_bubble\n");
}
cov->u_buffer.a.n = cov->tailIndex.a.n = 0;
@@ -27630,11 +27622,6 @@ bub_label_t* b_mask_t)
ma_ug_t *ug = NULL;
ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
// FILE* output_file = fopen("straw-debug.noseq.gfa", "w");
// ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
// fclose(output_file);
hap_cov_t *cov = NULL;
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);