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backup for hic

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chhylp123
2021-02-18 00:58:25 -05:00
parent d2ca12604b
commit e8b92f7a40
4 changed files with 309 additions and 16 deletions
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Overlaps.cpp
+89 -3
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@@ -11825,7 +11825,7 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
hc_links link;
///if(load_hc_links(&link, output_file_name) == 0)
if(load_hc_links(&link, output_file_name) == 0)
{
init_hc_links(&link, ug->g->n_seq, R_INF.total_reads);
asg_t *copy_sg = copy_read_graph(sg);
@@ -11841,7 +11841,7 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, &link);
///write_hc_links(&link, output_file_name);
write_hc_links(&link, output_file_name);
}
@@ -13779,9 +13779,11 @@ uint8_t is_final_check, float double_check_rate, uint8_t flag, float drop_rate)
if(R_INF.trio_flag[rId] == flag) flag_occ++;
if(R_INF.trio_flag[rId] != flag) non_flag_occ++;
}
if(is_final_check == 0 && hap_label_occ == u->n) continue;
///if(is_double_check && non_flag_occ < u->n*DOUBLE_CHECK_THRES) continue;
///if(is_double_check && non_flag_occ < u->n*double_check_rate) continue;
if(is_final_check)
{
if(non_flag_occ < u->n*double_check_rate) continue;
@@ -13813,10 +13815,12 @@ uint8_t is_final_check, float double_check_rate, uint8_t flag, float drop_rate)
if(non_flag_occ > ((non_flag_occ+flag_occ)*drop_rate))
{
if(if_primary_unitig(u, read_g, coverage_cut, sources, ruIndex, primary_flag))
{
continue;
}
if(u->m != 0)
{
u->circ = u->end = u->len = u->m = u->n = u->start = 0;
@@ -14429,7 +14433,8 @@ kvec_asg_arc_t_warp* new_rtg_edges)
renew_utg(ug, read_g, new_rtg_edges);
}
///if(flag == MOTHER) print_untig_by_read(*ug, "m64043_200627_000137/124716590/ccs", 2789716, NULL, NULL, "beg");
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 1,
FINAL_DOUBLE_CHECK_THRES, flag, drop_rate);
@@ -24046,6 +24051,87 @@ void minor_transitive_reduction_r_g(asg_t *r_g, asg_arc_t* rbub_edges, uint32_t
}
}
int if_recoverable(asg_t *sg, ma_ug_t *ug, bubble_type* bub, uint32_t bid, kvec_t_u32_warp* stack, uint8_t* vis_flag)
{
uint32_t beg_utg, sink_utg, *a = NULL, n, begRid, sinkRid, i;
get_bubbles(bub, bid, &beg_utg, &sink_utg, &a, &n, NULL);
if(beg_utg == (uint32_t)-1 || sink_utg == (uint32_t)-1) return 0;
if(beg_utg&1)
{
begRid = ug->u.a[beg_utg>>1].start^1;
}
else
{
begRid = ug->u.a[beg_utg>>1].end^1;
}
if(sink_utg&1)
{
sinkRid = ug->u.a[sink_utg>>1].start;
}
else
{
sinkRid = ug->u.a[sink_utg>>1].end;
}
asg_arc_t *acur = NULL;
uint32_t cur, ncur, v, n_vx = sg->n_seq<<1;
stack->a.n = 0;
memset(vis_flag, 0, n_vx);
kv_push(uint32_t, stack->a, begRid);
while (stack->a.n > 0)
{
stack->a.n--;
cur = stack->a.a[stack->a.n];
ncur = asg_arc_n(sg, cur);
acur = asg_arc_a(sg, cur);
vis_flag[cur] |= 1;
for (i = 0; i < ncur; i++)
{
if(acur[i].del) continue;
if(vis_flag[acur[i].v]&1) return 0;
if(vis_flag[acur[i].v^1]&1) return 0;
if(acur[i].v == sinkRid) continue;
kv_push(uint32_t, stack->a, acur[i].v);
}
}
vis_flag[sinkRid] |= 1;
begRid ^= 1; sinkRid ^= 1; v = begRid; begRid = sinkRid; sinkRid = v;
stack->a.n = 0;
kv_push(uint32_t, stack->a, begRid);
while (stack->a.n > 0)
{
stack->a.n--;
cur = stack->a.a[stack->a.n];
ncur = asg_arc_n(sg, cur);
acur = asg_arc_a(sg, cur);
vis_flag[cur] |= 2;
for (i = 0; i < ncur; i++)
{
if(acur[i].del) continue;
if(vis_flag[acur[i].v]&2) return 0;
if(vis_flag[acur[i].v]&1) return 0;
if(vis_flag[acur[i].v^1]&2) return 0;
if(acur[i].v == sinkRid) continue;
kv_push(uint32_t, stack->a, acur[i].v);
}
}
vis_flag[sinkRid] |= 2;
begRid ^= 1; sinkRid ^= 1; v = begRid; begRid = sinkRid; sinkRid = v;
return 1;
}
void rescue_bubbles_by_contained_reads(ma_ug_t *i_u_g, asg_t *r_g, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, uint32_t chainLenThres, uint32_t beg_idx, uint32_t occ, bubble_type* bub)
{