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chhylp123
2022-11-17 09:31:56 -05:00
parent 2c7b164f11
commit 9831afaf26
12 changed files with 1296 additions and 127 deletions
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hic.cpp
+12 -7
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@@ -16497,7 +16497,7 @@ void optimize_u_trans(kv_u_trans_t *ovlp, kvec_pe_hit* hits, ha_ug_index* idx)
}
}
kt_u_trans_t_idx(&k_trans, idx->ug->g->n_seq);
mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag, 1, NULL, 1, NULL, NULL, 1);
mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag, 1, NULL, 1, NULL, NULL, 1, 0);
for (i = m = 0; i < ovlp->n; i++){
x = &(ovlp->a[i]);
if(x->del) continue;
@@ -16524,7 +16524,7 @@ ha_ug_index* idx, uint64_t test_block_flip, uint64_t n_perturb)
__func__, test_block_flip, n_perturb);
renew_kv_u_trans(k_trans, link, &sl->hits, &(idx->t_ch->k_trans), idx, bub, s->s, NULL, 0);
mc_solve(NULL, NULL, k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
(bub->round_id == 0? 1 : 0), s->s, 1, NULL, test_block_flip?&(idx->t_ch->k_trans):0, 0);
(bub->round_id == 0? 1 : 0), s->s, 1, NULL, test_block_flip?&(idx->t_ch->k_trans):0, 0, 0);
}
@@ -16596,6 +16596,9 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
// label_unitigs_sm(s->s, NULL, idx->ug);
// goto skip_flipping;
// }
// print_debug_gfa(idx->read_g, idx->ug, opt->coverage_cut, "hic.phasing", opt->sources, opt->ruIndex,
// opt->max_hang, opt->min_ovlp, 0, 0, 0);
s = init_ps_t(11, idx->ug->g->n_seq);
// debug_round_test(s, 11, &bub, &k_trans, &link, &sl, idx, 1000, 10000);
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
@@ -16605,8 +16608,11 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
// if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s);
// update_trans_g(idx, &k_trans, &bub);
/*******************************for debug************************************/
// mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
// (bub.round_id == 0? 1 : 0), s->s, 1, (asm_opt.ar)?(&bub):(NULL), &(idx->t_ch->k_trans), 0,
// (((bub.round_id+1) == bub.n_round)?1:0));
mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
(bub.round_id == 0? 1 : 0), s->s, 1, /**&bub**/NULL, &(idx->t_ch->k_trans), 0);
(bub.round_id == 0? 1 : 0), s->s, 1, NULL, &(idx->t_ch->k_trans), 0, 0);
/*******************************for debug************************************/
label_unitigs_sm(s->s, NULL, idx->ug);
@@ -16639,9 +16645,8 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
///print_hc_links(&link, 0, &hap);
// print_kv_u_trans(&k_trans, &link, s->s);
///print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, idx->link, idx);
///print_hits(idx, &sl.hits, fn1);
// print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, NULL/**idx->link**/, idx);
// print_hits(idx, &sl.hits, fn1, fn2);
///print_debug_bubble_graph(&bub, idx->ug, asm_opt.output_file_name);
@@ -17369,4 +17374,4 @@ void hic_benchmark(ma_ug_t *ug, asg_t* read_g)
hic_short_align_bench(asm_opt.hic_reads[0], asm_opt.hic_reads[1], output_file_name, ug_index);
free(output_file_name);
}
}