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add "n-weight"

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chhylp123
2021-04-24 00:03:36 -04:00
parent 7b07e355b7
commit c972c64b39
5 changed files with 71 additions and 27 deletions
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CommandLines.cpp
+8 -2
View File
@@ -37,6 +37,7 @@ static ko_longopt_t long_options[] = {
{ "n-perturb", ko_required_argument, 323 },
{ "f-perturb", ko_required_argument, 324 },
{ "n-hap", ko_required_argument, 325 },
{ "n-weight", ko_required_argument, 326 },
{ 0, 0, 0 }
};
@@ -113,6 +114,10 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --h1 FILEs file names of Hi-C R1 [r1_1.fq,r1_2.fq,...]\n");
fprintf(stderr, " --h2 FILEs file names of Hi-C R2 [r2_1.fq,r2_2.fq,...]\n");
fprintf(stderr, " --seed INT RNG seed [%lu]\n", asm_opt->seed);
fprintf(stderr, " --n-weight INT\n");
fprintf(stderr, " rounds of reweighting Hi-C links [%d]\n", asm_opt->n_weight);
fprintf(stderr, " --n-perturb INT\n");
fprintf(stderr, " rounds of perturbation [%d]\n", asm_opt->n_perturb);
fprintf(stderr, " --f-perturb FLOAT\n");
@@ -188,8 +193,9 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->polyploidy = 2;
asm_opt->trio_flag_occ_thres = 60;
asm_opt->seed = 11;
asm_opt->n_perturb = 50000;
asm_opt->n_perturb = 10000;
asm_opt->f_perturb = 0.1;
asm_opt->n_weight = 3;
}
void destory_enzyme(enzyme* f)
@@ -651,6 +657,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 323) asm_opt->n_perturb = atoi(opt.arg);
else if (c == 324) asm_opt->f_perturb = atof(opt.arg);
else if (c == 325) asm_opt->polyploidy = atoi(opt.arg);
else if (c == 326) asm_opt->n_weight = atoi(opt.arg);
else if (c == 'l')
{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
@@ -682,6 +689,5 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
get_queries(argc, argv, &opt, asm_opt);
return check_option(asm_opt);
}
CommandLines.h
+1
View File
@@ -101,6 +101,7 @@ typedef struct {
uint64_t seed;
int32_t n_perturb;
double f_perturb;
int32_t n_weight;
} hifiasm_opt_t;
extern hifiasm_opt_t asm_opt;
hic.cpp
+18 -8
View File
@@ -2284,10 +2284,6 @@ uint32_t m_het_label, uint32_t p_het_label, uint32_t n_het_label)
hom_occ++;
}
}
// if(uid == 18759)
// {
// fprintf(stderr, "het_occ: %u, hom_occ: %u\n", het_occ, hom_occ);
// }
if((het_occ+hom_occ) == 0) return n_het_label; ///hom
if((het_occ > ((het_occ+hom_occ)*0.8)) && ((het_occ+hom_occ) > m_het_occ)) return m_het_label; ///must het
@@ -9271,7 +9267,7 @@ H_partition* hap, int8_t *s, trans_idx* dis)
dis->med = ((buf.n&1)?buf.a[buf.n>>1]:((buf.a[buf.n>>1]+buf.a[(buf.n>>1)-1])/2));
}
fprintf(stderr, "dis->med: %lu\n", dis->med);
// fprintf(stderr, "dis->med: %lu\n", dis->med);
kv_destroy(buf);
return 1;
@@ -13017,8 +13013,8 @@ void update_trans_g(ha_ug_index* idx, kv_u_trans_t *ta, bubble_type* bub)
// append_boundary_chain_hic(idx->ug, ta, bub);
fprintf(stderr, "s_bub: %lu, f_bub: %lu, b_bub: %lu, b_end_bub: %lu, tangle_bub: %lu, cross_bub: %lu, mess_bub: %lu\n",
bub->s_bub, bub->f_bub, bub->b_bub, bub->b_end_bub, bub->tangle_bub, bub->cross_bub, bub->mess_bub);
// fprintf(stderr, "s_bub: %lu, f_bub: %lu, b_bub: %lu, b_end_bub: %lu, tangle_bub: %lu, cross_bub: %lu, mess_bub: %lu\n",
// bub->s_bub, bub->f_bub, bub->b_bub, bub->b_end_bub, bub->tangle_bub, bub->cross_bub, bub->mess_bub);
///reorder_bubbles(bub, ta, idx->ug->g->n_seq);
// fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
@@ -14206,6 +14202,18 @@ void destory_ps_t(ps_t **s)
free((*s));
}
void verbose_het_stat(bubble_type *bub)
{
uint64_t i, hetBase = 0, homBase = 0;
for (i = 0; i < bub->ug->g->n_seq; i++)
{
if(IF_HOM(i, *bub)) homBase += bub->ug->g->seq[i].len;
else hetBase += bub->ug->g->seq[i].len;
}
fprintf(stderr, "[M::stat] # heterozygous bases: %lu; # homozygous bases: %lu\n", hetBase, homBase);
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
{
double index_time = yak_realtime();
@@ -14241,7 +14249,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
mb_nodes_t u;
kv_init(u.bid); kv_init(u.idx); kv_init(u.u);
memset(&bub, 0, sizeof(bubble_type));
bub.round_id = 0; bub.n_round = 2;
bub.round_id = 0; bub.n_round = asm_opt.n_weight;
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
identify_bubbles(idx->ug, &bub, idx->t_ch->is_r_het, &(idx->t_ch->k_trans));
@@ -14267,6 +14275,8 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
**/
}
verbose_het_stat(&bub);
///print_hc_links(&link, 0, &hap);
// print_kv_u_trans(&k_trans, &link, s->s);
hifiasm.1
+7 -2
View File
@@ -332,14 +332,19 @@ File names of input Hi-C R1 [r1_1.fq,r1_2.fq,...].
.BI --h2 \ FILEs
File names of input Hi-C R2 [r2_1.fq,r2_2.fq,...].
.TP
.BI --n-weight \ INT
Rounds of reweighting Hi-C links [3]. Increasing this may improves
phasing results but takes longer time.
.TP
.BI --n-perturb \ INT
Rounds of perturbation [50000]. Increasing this improves
Rounds of perturbation [10000]. Increasing this may improves
phasing results but takes longer time.
.TP
.BI --f-perturb \ FLOAT
Fraction to flip for perturbation [0.1]. Increasing this improves
Fraction to flip for perturbation [0.1]. Increasing this may improves
phasing results but takes longer time.
.TP
rcut.cpp
+37 -15
View File
@@ -9,6 +9,8 @@
#include "kthread.h"
#include "hic.h"
#define VERBOSE_CUT 0
#define mc_edge_key(e) ((e).x)
KRADIX_SORT_INIT(mce, mc_edge_t, mc_edge_key, member_size(mc_edge_t, x))
#define mb_edge_key(e) ((e).x)
@@ -2565,7 +2567,11 @@ void mb_solve_core(mc_opt_t *opt, mc_g_t *mg, kv_u_trans_t *ref, uint32_t is_sys
mb_g_t *mbg = init_mb_g_t(mg, ref, is_sys);
mb_svaux_t *bb;
/**************************init**************************/
fprintf(stderr, "\n\n\n\n\n*************beg-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
if(VERBOSE_CUT)
{
fprintf(stderr, "\n\n\n\n\n*************beg-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
}
mc_svaux_t *b;
mc_g_cc(mg->e);
b = mc_svaux_init(mg, opt->seed);
@@ -2576,11 +2582,17 @@ void mb_solve_core(mc_opt_t *opt, mc_g_t *mg, kv_u_trans_t *ref, uint32_t is_sys
/**************************init**************************/
mb_g_cc(mbg);
bb = mb_svaux_init(mbg, opt->seed);
/*******************************for debug************************************/
// print_mb_g_blcok(mbg);
fprintf(stderr, "*********before-[M::%s::mc_score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
fprintf(stderr, "*********before-[M::%s::mb_score->%f] ==> Partition\n", __func__, mb_score_all_advance(mg->e, mbg));
/*******************************for debug************************************/
if(VERBOSE_CUT)
{
fprintf(stderr, "*********before-[M::%s::mc_score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
fprintf(stderr, "*********before-[M::%s::mb_score->%f] ==> Partition\n", __func__, mb_score_all_advance(mg->e, mbg));
/*******************************for debug************************************/
// print_mb_g_blcok(mbg);
/*******************************for debug************************************/
}
opt->n_perturb = opt->n_b_perturb;
for (st = 0, i = 1; i <= mbg->e->n_seq; ++i) {
if (i == mbg->e->n_seq || mbg->e->cc[st]>>32 != mbg->e->cc[i]>>32) {
@@ -2589,13 +2601,15 @@ void mb_solve_core(mc_opt_t *opt, mc_g_t *mg, kv_u_trans_t *ref, uint32_t is_sys
}
}
opt->n_perturb = opt->n_s_perturb - opt->n_b_perturb;
/*******************************for debug************************************/
// debug_mb_solve_core(mbg);
fprintf(stderr, "*********after-[M::%s::mc_score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
fprintf(stderr, "*********after-[M::%s::mb_score->%f] ==> Partition\n", __func__, mb_score_all_advance(mg->e, mbg));
/*******************************for debug************************************/
mc_set_by_mbg(mg, mbg);
fprintf(stderr, "##############end-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
if(VERBOSE_CUT)
{
/*******************************for debug************************************/
// debug_mb_solve_core(mbg);
/*******************************for debug************************************/
fprintf(stderr, "##############end-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
}
destory_mb_g_t(&mbg);
mb_svaux_destroy(bb);
fprintf(stderr, "[M::%s::%.3f] ==> Partition\n", __func__, yak_realtime()-index_time);
@@ -2614,14 +2628,22 @@ void mc_solve_core(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub)
if(bp) mc_init_spin_all(opt, mg, NULL, b);
if(bp) mc_solve_bp(bp);
/*******************************for debug************************************/
fprintf(stderr, "\n\n\n\n\n*************beg-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
if(VERBOSE_CUT)
{
fprintf(stderr, "\n\n\n\n\n*************beg-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all_advance(mg->e, mg->s.a));
}
for (st = 0, i = 1; i <= mg->e->n_seq; ++i) {
if (i == mg->e->n_seq || mg->e->cc[st]>>32 != mg->e->cc[i]>>32) {
mc_solve_cc(opt, mg, b, st, i - st);
st = i;
}
}
fprintf(stderr, "##############end-[---M::%s::score->%f] ==> Partition\n", __func__, mc_score_all(mg->e, b));
if(VERBOSE_CUT)
{
fprintf(stderr, "##############end-[---M::%s::score->%f] ==> Partition\n", __func__, mc_score_all(mg->e, b));
}
if(bp) mc_solve_bp(bp);
///mc_write_info(g, b);
mc_svaux_destroy(b);
@@ -2796,7 +2818,7 @@ void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_u
mb_solve_core(&opt, mg, ref, is_sys);
///debug_mc_g_t(mg);
if(renew_s == 0) write_mc_g_t(&opt, mg, MC_NAME);
// if(renew_s == 0) write_mc_g_t(&opt, mg, MC_NAME);
mc_solve_core(&opt, mg, bub);
if((asm_opt.flag & HA_F_PARTITION) && t_ch)