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update v0.10

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chhylp123
2020-07-31 12:23:25 -04:00
parent ace34ae2b8
commit 9d659fd2e0
2 changed files with 10 additions and 99 deletions
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Overlaps.cpp
+9 -98
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@@ -12869,29 +12869,12 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
uint32_t is_first = 1;
redo:
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "beg");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "beg");
///print_untig((ug), 61955, "i-0:", 0);
asg_pop_bubble_primary_trio(ug, bubble_dist, trio_flag, DROP);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "beg-1");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "beg-1");
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "beg-2");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "beg-2");
magic_trio_phasing(g, ug, read_g, coverage_cut, sources, reverse_sources, 2, ruIndex, trio_flag, trio_drop_rate);
magic_trio_phasing(g, ug, read_g, coverage_cut, sources, reverse_sources, 2, ruIndex, trio_flag, trio_drop_rate);
///drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "111");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "111");
/**********debug**********/
if(just_bubble_pop == 0)
{
@@ -12899,19 +12882,11 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
cut_trio_tip_primary(g, ug, tipsLen, trio_flag, 0, read_g, reverse_sources, ruIndex,
2);
}
// print_read_all(ug, "m64011_190901_095311/1442493/ccs", "**convex**");
// print_read_all(ug, "m64011_190830_220126/173672768/ccs", "**kept**");
// print_read_all(ug, "m64011_190901_095311/6621017/ccs", "**missed**");
/**********debug**********/
long long pre_cons = get_graph_statistic(g);
long long cur_cons = 0;
while(pre_cons != cur_cons)
{
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "222");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "222");
pre_cons = get_graph_statistic(g);
///need consider tangles
///asg_pop_bubble_primary(g, bubble_dist);
@@ -12920,41 +12895,15 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
if(just_bubble_pop == 0)
{
///need consider tangles
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex,
2, tip_drop_ratio);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "333");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "333");
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, trio_flag);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "444");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "444");
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, trio_flag);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex,
2, tip_drop_ratio, stops_threshold);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "555");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "555");
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources,
2, ruIndex, stops_threshold);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "666");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "666");
///print_debug_gfa(read_g, ug, coverage_cut, "debug_chimeric", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate,
ruIndex);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "666-2");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "666-2");
///need consider tangles
///note we need both the read graph and the untig graph
}
@@ -12963,9 +12912,6 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
}
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "777");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "777");
if(just_bubble_pop == 0)
{
///asg_cut_tip_primary(g, ug, tipsLen);
@@ -12973,26 +12919,10 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
2);
}
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "888");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "888");
resolve_tangles(ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, trio_flag, drop_ratio);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "999");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "999");
resolve_tangles(ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, trio_flag, drop_ratio);
drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "101010");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "101010");
all_to_all_deduplicate(ug, read_g, coverage_cut, sources, trio_flag, trio_drop_rate, reverse_sources, ruIndex, DOUBLE_CHECK_THRES);
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "111111");
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "111111");
if(is_first)
{
is_first = 0;
@@ -13716,19 +13646,8 @@ long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long stops_
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
kvec_asg_arc_t_warp* new_rtg_edges)
{
// if(flag == MOTHER)
// {
// print_debug_gfa(read_g, *ug, coverage_cut, "debug_hap2", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
// }
print_untig_by_read(*ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "0-beg");
print_untig_by_read(*ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "0-beg");
asg_t* nsg = (*ug)->g;
uint32_t v, n_vtx = nsg->n_seq;
//if(flag == MOTHER) print_untig_by_read(*ug, "m54329U_190617_231905/65340614/ccs", (uint32_t)-1, sources, reverse_sources, "beg1");
//if(flag == MOTHER) print_untig_by_read(*ug, "m54329U_190827_173812/67108993/ccs", (uint32_t)-1, sources, reverse_sources, "beg2");
/**
kvec_t_u32_warp new_rtg_nodes;
kv_init(new_rtg_nodes.a);
@@ -13757,15 +13676,11 @@ kvec_asg_arc_t_warp* new_rtg_edges)
///primary_flag = get_utg_attributes(*ug, read_g, coverage_cut, sources, ruIndex);
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 0,
DOUBLE_CHECK_THRES, flag, drop_rate);
print_untig_by_read(*ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "1-beg");
print_untig_by_read(*ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "1-beg");
adjust_utg_advance(read_g, (*ug), reverse_sources, ruIndex);
nsg = (*ug)->g;
n_vtx = nsg->n_seq;
for (v = 0; v < n_vtx; ++v)
@@ -13774,10 +13689,6 @@ kvec_asg_arc_t_warp* new_rtg_edges)
nsg->seq[v].c = PRIMARY_LABLE;
EvaluateLen((*ug)->u, v) = (*ug)->u.a[v].n;
}
print_untig_by_read(*ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "2-beg");
print_untig_by_read(*ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "2-beg");
clean_trio_untig_graph(*ug, read_g, coverage_cut, sources, reverse_sources, bubble_dist,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, NULL, NULL, 0, 0, 0,
chimeric_rate, 0, 0, drop_ratio, flag, drop_rate);
@@ -26892,9 +26803,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
normalize_ma_hit_t_single_side_advance(sources, n_read);
normalize_ma_hit_t_single_side_advance(reverse_sources, n_read);
// debug_info_of_specfic_read("m64062_190803_042216/122882911/ccs", sources, reverse_sources,
// -1, "clean");
if (ha_opt_triobin(&asm_opt))
{
@@ -26920,6 +26828,9 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///just need to deal with trio here
ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
// debug_info_of_specfic_read("m54329U_190617_231905/176226420/ccs", sources, reverse_sources,
// -1, "clean");
sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
asg_arc_del_trans(sg, gap_fuzz);
asm_opt.coverage = get_coverage(sources, coverage_cut, n_read);