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upadate man-page and readme

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This commit is contained in:
Haoyu Cheng
2020-01-04 11:54:08 +08:00
parent 1e46798bfb
commit d8416873f3
7 changed files with 407 additions and 176 deletions
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Overlaps.cpp
+52 -131
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@@ -25,8 +25,8 @@ KRADIX_SORT_INIT(arch64, uint64_t, generic_key, 8)
KSORT_INIT_GENERIC(uint32_t)
///actually min_thres = MAX_SHORT_TIPS + 1 there are MAX_SHORT_TIPS reads
long long min_thres = MAX_SHORT_TIPS + 1;
///this value has been updated at the first line of build_string_graph_without_clean
long long min_thres;
void ma_hit_sort_tn(ma_hit_t *a, long long n)
{
@@ -530,7 +530,7 @@ void ma_hit_contained(ma_hit_t_alloc* sources, long long n_read, ma_sub_t *cover
//check the corresponding two reads
ma_sub_t *sq = &(coverage_cut[Get_qn(*h)]);
ma_sub_t *st = &(coverage_cut[Get_tn(*h)]);
r = ma_hit2arc(h, sq->e - sq->s, st->e - st->s, max_hang, MAX_HANG_PRE, min_ovlp, &t);
r = ma_hit2arc(h, sq->e - sq->s, st->e - st->s, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
///r could not be MA_HT_SHORT_OVLP or MA_HT_INT
if (r == MA_HT_QCONT)
{
@@ -598,9 +598,10 @@ void ma_hit_flt(ma_hit_t_alloc* sources, long long n_read, ma_sub_t *coverage_cu
/**note!!! h->qn and h->qs have been normalized by sq->s
* h->ts and h->tn have been normalized by sq->e
**/
///here the max_hang = 1000, MAX_HANG_PRE = 0.8, min_ovlp = 500
///here the max_hang = 1000, asm_opt.max_hang_rate = 0.8, min_ovlp = 50
///for me, there should not have any overhang..so r cannot be equal to MA_HT_INT
r = ma_hit2arc(h, sq->e - sq->s, st->e - st->s, max_hang, MAX_HANG_PRE, min_ovlp, &t);
///sq->e - sq->s = the length of query; st->e - st->s = the length od target
r = ma_hit2arc(h, sq->e - sq->s, st->e - st->s, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
///for me, there should not have any overhang..so r cannot be equal to MA_HT_INT
@@ -1138,7 +1139,7 @@ long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut, float shift_rate)
void ma_hit_cut(int min_dp, ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
void ma_hit_cut(ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
long long mini_overlap_length, ma_sub_t** coverage_cut)
{
double startTime = Get_T();
@@ -1491,7 +1492,7 @@ int max_hang, int min_ovlp)
int ql = coverage_cut[Get_qn(*h)].e - coverage_cut[Get_qn(*h)].s;
//high coverage region [sub[qn].e, sub[qn].s) in target
int tl = coverage_cut[Get_tn(*h)].e - coverage_cut[Get_tn(*h)].s;
r = ma_hit2arc(h, ql, tl, max_hang, MAX_HANG_PRE, min_ovlp, &t);
r = ma_hit2arc(h, ql, tl, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
/**
#define MA_HT_INT (-1)
#define MA_HT_QCONT (-2)
@@ -6139,7 +6140,6 @@ int asg_arc_del_tri_link(asg_t *g, int max_dist)
}
else if(f1)
{
if(l1 <= min_thres)
{
continue;
@@ -6148,7 +6148,6 @@ int asg_arc_del_tri_link(asg_t *g, int max_dist)
}
else if(f2)
{
if(l2 <= min_thres)
{
continue;
@@ -8724,35 +8723,6 @@ long long asg_arc_del_self_circle_untig(asg_t *g, long long circleLen, int is_dr
void output_unitig_graph_without_small_bubbles(asg_t *sg, ma_sub_t* coverage_cut,
char* output_file_name, long long n_read, long long bubble_dist, long long tipsLen)
{
asg_cut_tip(sg, tipsLen);
asg_pop_bubble(sg, bubble_dist);
asg_cut_tip(sg, tipsLen);
ma_ug_t *ug = NULL;
ug = ma_ug_gen(sg);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.no_s_bub.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
sprintf(gfa_name, "%s.simple.no_s_bub.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
}
void output_unitig_graph_without_small_bubbles_primary(asg_t *sg, ma_sub_t* coverage_cut,
char* output_file_name, long long n_read, long long bubble_dist, long long tipsLen)
{
@@ -8782,57 +8752,6 @@ char* output_file_name, long long n_read, long long bubble_dist, long long tipsL
void output_contig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name, long long n_read, long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long circleLen,
ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
{
asg_cut_tip(sg, tipsLen);
// asg_pop_bubble(sg, bubble_dist);
// asg_arc_del_self_circle_untig(sg, circleLen);
long long n_ac = 1;
long long pre_cons = sg->n_seq + sg->n_arc;
long long cur_cons = 0;
///while(n_ac > 0)
while(pre_cons != cur_cons)
{
pre_cons = sg->n_seq + sg->n_arc;
n_ac = 0;
n_ac += asg_pop_bubble(sg, bubble_dist);
n_ac += asg_arc_del_self_circle_untig(sg, circleLen, 0);
n_ac += asg_arc_cut_long_tip(sg, tip_drop_ratio);
n_ac += asg_arc_cut_long_equal_tips(sg, reverse_sources, 2);
cur_cons = sg->n_seq + sg->n_arc;
}
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
///asg_arc_del_self_circle_untig(sg, circleLen);
ma_ug_t *ug = NULL;
ug = ma_ug_gen(sg);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.contig.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
sprintf(gfa_name, "%s.simple.contig.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
}
long long get_graph_statistic(asg_t *g)
{
long long num_arc = 0;
@@ -8848,7 +8767,7 @@ long long get_graph_statistic(asg_t *g)
}
void output_contig_graph_primary(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name, long long n_read, long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long circleLen,
ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
ma_hit_t_alloc* reverse_sources)
{
asg_cut_tip_primary(sg, tipsLen);
long long n_ac = 1;
@@ -8870,7 +8789,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
asg_arc_identify_simple_bubbles_multi(sg, 1);
///we don't need a special function here since it just removes edges instead of nodes
asg_arc_del_short_false_link_primary(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
asg_arc_del_short_false_link_primary(sg, 0.6, 0.85, bubble_dist, reverse_sources, asm_opt.max_short_tip);
ma_ug_t *ug = NULL;
@@ -9221,10 +9140,13 @@ long long rescue_threshold)
void build_string_graph_without_clean(
int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
long long max_hang_length, long long clean_round, long long pop_bubble_size,
long long max_hang_length, long long clean_round, long long gap_fuzz,
float min_ovlp_drop_ratio, float max_ovlp_drop_ratio, char* output_file_name,
long long bubble_dist, int read_graph, int write)
{
///actually min_thres = asm_opt.max_short_tip + 1 there are asm_opt.max_short_tip reads
min_thres = asm_opt.max_short_tip + 1;
if (asm_opt.write_index_to_disk && write)
{
write_all_data_to_disk(sources, reverse_sources,
@@ -9242,13 +9164,13 @@ long long bubble_dist, int read_graph, int write)
ma_hit_sub(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
detect_chimeric_reads(sources, reverse_sources, n_read, readLen, coverage_cut,
FINAL_OVERLAP_ERROR_RATE*2);
ma_hit_cut(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
ma_hit_cut(sources, n_read, readLen, mini_overlap_length, &coverage_cut);
///it seems we do not need ma_hit_flt
ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
ma_hit_contained(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
asg_t *sg = NULL;
sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
asg_arc_del_trans(sg, GAP_FUZZ);
asg_arc_del_trans(sg, gap_fuzz);
if(VERBOSE >= 1)
@@ -9261,14 +9183,14 @@ long long bubble_dist, int read_graph, int write)
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_cut_tip(sg, asm_opt.max_short_tip);
// debug_info_of_specfic_node("m64016_190918_162737/72220752/ccs", sg, "cut_tip");
///asg_arc_del_short_diploid_unclean(sg, corase_ovlp_drop_ratio, sources, reverse_sources);
// asg_arc_del_single_node_bubble(sg, bubble_dist);
// asg_cut_tip(sg, MAX_SHORT_TIPS);
///asg_cut_tip(sg, MAX_SHORT_TIPS);
// asg_cut_tip(sg, asm_opt.max_short_tip);
///asg_cut_tip(sg, asm_opt.max_short_tip);
if(clean_round > 0)
{
@@ -9303,11 +9225,11 @@ long long bubble_dist, int read_graph, int write)
int tri_flag = 0;
tri_flag += asg_arc_del_self_circle_contig(sg);
///asg_arc_del_single_node_bubble(sg, bubble_dist);
tri_flag += asg_arc_del_single_node_directly(sg, MAX_SHORT_TIPS, sources);
tri_flag += asg_arc_del_single_node_directly(sg, asm_opt.max_short_tip, sources);
tri_flag += asg_arc_del_triangular_advance(sg, bubble_dist);
tri_flag += asg_arc_del_cross_bubble(sg, bubble_dist);
///asg_arc_del_single_node_bubble(sg, bubble_dist);
tri_flag += asg_arc_del_single_node_directly(sg, MAX_SHORT_TIPS, sources);
tri_flag += asg_arc_del_single_node_directly(sg, asm_opt.max_short_tip, sources);
if(tri_flag == 0)
{
break;
@@ -9315,37 +9237,38 @@ long long bubble_dist, int read_graph, int write)
}
///asg_arc_del_orthology(sg, reverse_sources, drop_ratio, MAX_SHORT_TIPS);
// asg_arc_del_orthology_multiple_way(sg, reverse_sources, drop_ratio, MAX_SHORT_TIPS);
// asg_cut_tip(sg, MAX_SHORT_TIPS);
///asg_arc_del_orthology(sg, reverse_sources, drop_ratio, asm_opt.max_short_tip);
// asg_arc_del_orthology_multiple_way(sg, reverse_sources, drop_ratio, asm_opt.max_short_tip);
// asg_cut_tip(sg, asm_opt.max_short_tip);
/****************************may have bugs********************************/
asg_arc_identify_simple_bubbles_multi(sg, 1);
//reomve edge between two chromesomes
asg_arc_del_false_node(sg, MAX_SHORT_TIPS);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_arc_del_false_node(sg, asm_opt.max_short_tip);
asg_cut_tip(sg, asm_opt.max_short_tip);
/****************************may have bugs********************************/
/****************************may have bugs********************************/
///asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_identify_simple_bubbles_multi(sg, 0);
///asg_arc_del_short_diploid_unclean_exact(sg, drop_ratio, sources);
asg_arc_del_short_diploid_by_exact(sg, MAX_SHORT_TIPS, sources);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_arc_del_short_diploid_by_exact(sg, asm_opt.max_short_tip, sources);
asg_cut_tip(sg, asm_opt.max_short_tip);
/****************************may have bugs********************************/
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_short_diploid_by_length(sg, drop_ratio, MAX_SHORT_TIPS, reverse_sources, MAX_SHORT_TIPS);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_arc_del_short_diploid_by_length(sg, drop_ratio, asm_opt.max_short_tip, reverse_sources,
asm_opt.max_short_tip);
asg_cut_tip(sg, asm_opt.max_short_tip);
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, asm_opt.max_short_tip);
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_complex_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
asg_arc_del_complex_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, asm_opt.max_short_tip);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_cut_tip(sg, asm_opt.max_short_tip);
}
}
@@ -9358,10 +9281,10 @@ long long bubble_dist, int read_graph, int write)
{
int tri_flag = 0;
tri_flag += asg_arc_del_self_circle_contig(sg);
tri_flag += asg_arc_del_single_node_directly(sg, MAX_SHORT_TIPS, sources);
tri_flag += asg_arc_del_single_node_directly(sg, asm_opt.max_short_tip, sources);
tri_flag += asg_arc_del_triangular_advance(sg, bubble_dist);
tri_flag += asg_arc_del_cross_bubble(sg, bubble_dist);
tri_flag += asg_arc_del_single_node_directly(sg, MAX_SHORT_TIPS, sources);
tri_flag += asg_arc_del_single_node_directly(sg, asm_opt.max_short_tip, sources);
if(tri_flag == 0)
{
@@ -9371,32 +9294,32 @@ long long bubble_dist, int read_graph, int write)
asg_arc_del_short_diploi_by_suspect_edge(sg, MAX_SHORT_TIPS, sources);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_arc_del_triangular_directly(sg, MAX_SHORT_TIPS, reverse_sources);
asg_arc_del_short_diploi_by_suspect_edge(sg, asm_opt.max_short_tip, sources);
asg_cut_tip(sg, asm_opt.max_short_tip);
asg_arc_del_triangular_directly(sg, asm_opt.max_short_tip, reverse_sources);
///asg_arc_identify_simple_bubbles_multi(sg, 0);
// asg_arc_del_chimeric_read(sg, MAX_SHORT_TIPS*2);
// asg_cut_tip(sg, MAX_SHORT_TIPS);
// asg_arc_del_chimeric_read(sg, asm_opt.max_short_tip*2);
// asg_cut_tip(sg, asm_opt.max_short_tip);
asg_arc_identify_simple_bubbles_multi(sg, 0);
asg_arc_del_orthology_multiple_way(sg, reverse_sources, 0.4, MAX_SHORT_TIPS);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_arc_del_orthology_multiple_way(sg, reverse_sources, 0.4, asm_opt.max_short_tip);
asg_cut_tip(sg, asm_opt.max_short_tip);
asg_arc_identify_simple_bubbles_multi(sg, 0);
asg_arc_del_too_short_overlaps(sg, 2000, min_ovlp_drop_ratio, reverse_sources, MAX_SHORT_TIPS);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_arc_del_too_short_overlaps(sg, 2000, min_ovlp_drop_ratio, reverse_sources, asm_opt.max_short_tip);
asg_cut_tip(sg, asm_opt.max_short_tip);
/**
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_short_false_link_advance(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
asg_arc_del_short_false_link_advance(sg, 0.6, 0.85, bubble_dist, reverse_sources, asm_opt.max_short_tip);
**/
@@ -9435,7 +9358,7 @@ long long bubble_dist, int read_graph, int write)
asg_arc_identify_simple_bubbles_multi(sg, 0);
c_tips += asg_arc_del_complex_false_link(sg, 0.7, bubble_dist);
if(c_tips) asg_cut_tip(sg, MAX_SHORT_TIPS);
if(c_tips) asg_cut_tip(sg, asm_opt.max_short_tip);
i++;
}
**/
@@ -9444,15 +9367,13 @@ long long bubble_dist, int read_graph, int write)
/**
memset(sg->seq_vis, 0, sg->n_seq*2*sizeof(uint8_t));
asg_arc_del_short_diploid_by_exact(sg, MAX_SHORT_TIPS, sources);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_arc_del_short_diploid_by_exact(sg, asm_opt.max_short_tip, sources);
asg_cut_tip(sg, asm_opt.max_short_tip);
**/
// debug_info_of_specfic_node("m64016_190918_162737/141297762/ccs", sg);
///out:
///output_tips(sg, &R_INF);
///check_node_lable(sg);
output_unitig_graph(sg, coverage_cut, output_file_name, n_read);
@@ -9463,9 +9384,9 @@ long long bubble_dist, int read_graph, int write)
}
output_unitig_graph_without_small_bubbles_primary(sg, coverage_cut, output_file_name, n_read,
pop_bubble_size, MAX_SHORT_TIPS);
output_contig_graph_primary(sg, coverage_cut, output_file_name, n_read, 10000000, MAX_SHORT_TIPS, 0.1, 20,
reverse_sources, MAX_SHORT_TIPS);
asm_opt.small_pop_bubble_size, asm_opt.max_short_tip);
output_contig_graph_primary(sg, coverage_cut, output_file_name, n_read, bubble_dist,
asm_opt.max_short_tip, 0.1, 20, reverse_sources);
output_contig_graph_alternative(sg, coverage_cut, output_file_name, n_read);