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better seeding

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chhylp123
2021-08-22 09:53:34 -04:00
parent bfff640a82
commit 37b07e4d33
15 changed files with 637 additions and 406 deletions
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Purge_Dups.cpp
+13 -20
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@@ -176,6 +176,7 @@ long long* hom_peak, long long* het_peak, long long* k_mer_only, long long* cove
///if the second peak is not significant
if(max2 < max * 0.05 || min > max2 * 0.95) max2 = max2_i = -1;
}
if(max2 < max*0.0075) max2 = max2_i = -1;
// look for smaller peak on the high end
@@ -205,7 +206,7 @@ long long* hom_peak, long long* het_peak, long long* k_mer_only, long long* cove
if (max3 < max * 0.05 || min > max3 * 0.95 || max3_i > max_i * 3) max3 = max3_i = -1;
}
if (max3 < max*0.0075) max3 = max3_i = -1;
@@ -216,6 +217,13 @@ long long* hom_peak, long long* het_peak, long long* k_mer_only, long long* cove
topo_peak = cov_buf[topo_peak_i];
if (topo_peak <= max * 0.05) topo_peak_i = topo_peak = -1;
}
if(asm_opt.purge_level_primary == 0)
{
(*hom_peak) = max_i;
return;
}
long long k_mer_het, k_mer_hom, coverage_het, coverage_hom, alter_peak;
k_mer_het = k_mer_hom = coverage_het = coverage_hom = alter_peak = -1;
@@ -345,12 +353,6 @@ ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, long long cov_buf_length)
}
}
// if(qn == 1893151 || qn == 1929038)
// {
// fprintf(stderr, "qn: %lu, C_bases_primary: %lld, C_bases_alter: %lld, C_bases: %lld\n",
// qn, C_bases_primary, C_bases_alter, C_bases);
// }
C_bases = C_bases_primary + C_bases_alter;
if(C_bases_alter < C_bases * ALTER_COV_THRES) continue;
@@ -369,8 +371,6 @@ ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, long long cov_buf_length)
}
}
///fprintf(stderr, "alter max_i: %lld, max: %lld\n", max_i, max);
///if(max_i < 5) max_i = max = -1;
if(alter_bases < primary_bases * REAL_ALTER_THRES) max_i = max = -1;
free(cov_buf);
@@ -4981,9 +4981,9 @@ void debug_p_g_t(p_g_t* pg, hap_cov_t *cov, asg_t *read_g)
offset += (uint32_t)u->a[i];
if(i >= sid && i <= eid)
{
if(cov->t_ch->is_r_het[u->a[i]>>33] != t->h_status)
if(cov->t_ch->ir_het[u->a[i]>>33] != t->h_status)
{
fprintf(stderr, "ERROR-(-3): is_r_het: %u, h_status: %u\n", cov->t_ch->is_r_het[u->a[i]>>33], t->h_status);
fprintf(stderr, "ERROR-(-3): is_r_het: %u, h_status: %u\n", cov->t_ch->ir_het[u->a[i]>>33], t->h_status);
}
}
}
@@ -5065,11 +5065,11 @@ p_g_t *init_p_g_t(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
for (k = 1, l = 0, offset = 0, l_pos = 0; k <= u->n; ++k)
{
///if (k == u->n || (!!cov->t_ch->is_r_het[u->a[k]>>33]) != (!!cov->t_ch->is_r_het[u->a[l]>>33]))
if (k == u->n || cov->t_ch->is_r_het[u->a[k]>>33] != cov->t_ch->is_r_het[u->a[l]>>33])
if (k == u->n || cov->t_ch->ir_het[u->a[k]>>33] != cov->t_ch->ir_het[u->a[l]>>33])
{
kv_pushp(p_node_t, pg->pg_het_node, &t);
t->c_ug_id = uId;
t->h_status = cov->t_ch->is_r_het[u->a[l]>>33];
t->h_status = cov->t_ch->ir_het[u->a[l]>>33];
t->baseBeg = l_pos;
t->baseEnd = offset + read_g->seq[u->a[k-1]>>33].len - 1;
t->nodeBeg = l;
@@ -5261,7 +5261,6 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t colle
init_hap_overlaps_list(&all_ovlp, nsg->n_seq);
hap_overlaps_list back_all_ovlp;
init_hap_overlaps_list(&back_all_ovlp, nsg->n_seq);
///uint32_t junk_cov, hap_cov, dip_cov, junk_occ, repeat_occ, single_cov;
asg_arc_t t, *p = NULL;
int r;
hap_alignment_struct_pip hap_buf;
@@ -5382,12 +5381,6 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t colle
r = get_hap_arch(&(all_ovlp.x[uId].a.a[i]), ug->u.a[all_ovlp.x[uId].a.a[i].xUid].len,
ug->u.a[all_ovlp.x[uId].a.a[i].yUid].len, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
// if(all_ovlp.x[uId].a.a[i].xUid == 118 && all_ovlp.x[uId].a.a[i].yUid == 82)
// {
// fprintf(stderr, "r: %d\n", r);
// print_hap_paf(ug, &(all_ovlp.x[uId].a.a[i]));
// }
if(r < 0) continue;
p = asg_arc_pushp(pg->pg_h_lev);
*p = t;