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backup phasing

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chhylp123
2021-05-31 04:19:05 -04:00
parent e774a83be2
commit aa164949f2
5 changed files with 71 additions and 55 deletions
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rcut.cpp
+47 -30
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@@ -611,13 +611,13 @@ mb_nodes_t *update_mb_nodes_t(kv_u_trans_t *ref, mc_match_t* ma, uint32_t occ)
return x;
}
mb_g_t *init_mb_g_t(mc_g_t *mg, kv_u_trans_t *ref, uint32_t is_sys)
mb_g_t *init_mb_g_t(mc_match_t* e, kv_u_trans_t *ref, uint32_t is_sys)
{
mc_edge_t *o = NULL;
uint32_t i, k, m, n, a_n[2], *a[2], qn, tn, qb, tb;
mb_edge_t *t = NULL;
mb_g_t *p = NULL; CALLOC(p, 1);
p->u = update_mb_nodes_t(ref, mg->e, mg->ug->g->n_seq);
p->u = update_mb_nodes_t(ref, e, e->n_seq);
p->e = NULL; CALLOC(p->e, 1);
p->e->n_seq = p->u->u.n;
kv_init(p->e->ma); kv_init(p->e->idx);
@@ -629,8 +629,8 @@ mb_g_t *init_mb_g_t(mc_g_t *mg, kv_u_trans_t *ref, uint32_t is_sys)
for (k = 0; k < a_n[0]; k++)
{
qn = a[0][k];
o = pt_a(*(mg->e), qn);
n = pt_n(*(mg->e), qn);
o = pt_a(*e, qn);
n = pt_n(*e, qn);
for (m = 0; m < n; m++)
{
tn = ma_y(o[m]);
@@ -650,8 +650,8 @@ mb_g_t *init_mb_g_t(mc_g_t *mg, kv_u_trans_t *ref, uint32_t is_sys)
for (k = 0; k < a_n[1]; k++)
{
qn = a[1][k];
o = pt_a(*(mg->e), qn);
n = pt_n(*(mg->e), qn);
o = pt_a(*e, qn);
n = pt_n(*e, qn);
for (m = 0; m < n; m++)
{
tn = ma_y(o[m]);
@@ -2152,10 +2152,7 @@ uint32_t mc_solve_cc(const mc_opt_t *opt, const mc_g_t *mg, mc_svaux_t *b, uint3
}
}
fprintf(stderr, "\nBeg-[M::%s::score->%f]\n", __func__, mc_score(mg->e, b));
print_mc_node(mg->e, b, 3838);
print_mc_node(mg->e, b, 36880);
// print_mc_node(mg->e, b, 36880);
// print_sc(opt, mg, b, sc_opt, n_iter);
// mc_reset_z_debug(mg->e, b);
// print_sc(opt, mg->e, b, sc_opt, n_iter);
@@ -2189,10 +2186,6 @@ uint32_t mc_solve_cc(const mc_opt_t *opt, const mc_g_t *mg, mc_svaux_t *b, uint3
}
sc_opt = sc;
}
fprintf(stderr, "\n");
print_mc_node(mg->e, b, 3838);
print_mc_node(mg->e, b, 36880);
}
for (j = 0; j < b->cc_size; ++j)
@@ -2200,8 +2193,7 @@ uint32_t mc_solve_cc(const mc_opt_t *opt, const mc_g_t *mg, mc_svaux_t *b, uint3
b->s[b->cc_node[j]] = b->s_opt[b->cc_node[j]];
b->z[b->cc_node[j]] = b->z_opt[b->cc_node[j]];
}
fprintf(stderr, "End-[M::%s::score->%f]\n", __func__, mc_score(mg->e, b));
return n_iter;
}
@@ -2594,7 +2586,7 @@ void mb_solve_core(mc_opt_t *opt, mc_g_t *mg, kv_u_trans_t *ref, uint32_t is_sys
if(!ref) return;
double index_time = yak_realtime();
uint32_t st, i;
mb_g_t *mbg = init_mb_g_t(mg, ref, is_sys);
mb_g_t *mbg = init_mb_g_t(mg->e, ref, is_sys);
mb_svaux_t *bb;
/**************************init**************************/
if(VERBOSE_CUT)
@@ -2859,7 +2851,7 @@ void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_u
mc_g_t *mg = init_mc_g_t(ug, read_g, s, renew_s);
update_mc_edges(mg, ovlp, ta, t_ch, f_rate, is_sys);
fprintf(stderr, "[M::%s:: # edges: %u]\n", __func__, (uint32_t)mg->e->ma.n);
// fprintf(stderr, "[M::%s:: # edges: %u]\n", __func__, (uint32_t)mg->e->ma.n);
mb_solve_core(&opt, mg, ref, is_sys);
///debug_mc_g_t(mg);
@@ -2873,7 +2865,7 @@ void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_u
if(ovlp) clean_ovlp_by_mc(mg, ovlp);
print_hap_s(s, ug->u.n);
// print_hap_s(s, ug->u.n);
destory_mc_g_t(&mg);
}
@@ -3237,19 +3229,19 @@ t_w_t mcgg_init_spin(const mc_match_t *ma, mcgg_svaux_t *b)
uint32_t n1 = ma_x(*e), n2 = ma_y(*e);
if (b->s[n1].s == 0 && b->s[n2].s == 0) {
b->s[n1].s = kr_drand_node(n1, b, &(b->s[n1].hc));
debug_hapM(&(b->s[n1]), "s0");
// debug_hapM(&(b->s[n1]), "s0");
b->s[n2].s = kr_drand_node_ref(n2, b, &(b->s[n2].hc), b->s[n1].s, e->w>0?1:0);
debug_hapM(&(b->s[n2]), "s1");
// debug_hapM(&(b->s[n2]), "s1");
}
else if(b->s[n1].s == 0)
{
b->s[n1].s = kr_drand_node_ref(n1, b, &(b->s[n1].hc), b->s[n2].s, e->w>0?1:0);
debug_hapM(&(b->s[n1]), "s2");
// debug_hapM(&(b->s[n1]), "s2");
}
else if(b->s[n2].s == 0)
{
b->s[n2].s = kr_drand_node_ref(n2, b, &(b->s[n2].hc), b->s[n1].s, e->w>0?1:0);
debug_hapM(&(b->s[n2]), "s3");
// debug_hapM(&(b->s[n2]), "s3");
}
}
@@ -3354,19 +3346,40 @@ void inline back_status(mcgg_svaux_t *b, uint32_t id, uint32_t to_opt)
}
}
/**
static inline mcg_node_t kr_drand_node_new(uint64_t id, mcgg_svaux_t *b)
{
if(id == 10070) fprintf(stderr, "id-%lu, h[0]-%u, h[1]-%u\n", id, b->s[id].h[0], b->s[id].h[1]);
uint32_t hn = b->s[id].h[0]-1, is_old = 1, k;
if((b->s[id].h[1] != (uint16_t)-1) && (kr_drand_r(&b->x) > b->s[id].hw[0]))
{
hn = b->s[id].h[1]-1; is_old = 0;
}
if(id == 10070) fprintf(stderr, "id-%lu, hn-%u, b->m[hn].n-%u, is_old-%u\n", id, hn, b->m[hn].n, is_old);
b->x = kr_splitmix64(b->x);
k = b->x%(b->m[hn].n-is_old);
if(id == 10070) fprintf(stderr, "id-%lu, hn-%u, k-%u\n", id, hn, k);
if(b->m[hn].a[k] == b->s[id].s) k = b->m[hn].n-1;
return b->m[hn].a[k];
}
**/
static inline mcg_node_t kr_drand_node_new(uint64_t id, mcgg_svaux_t *b)
{
uint32_t hn = b->s[id].h[0]-1, k;
if((b->s[id].h[1] != (uint16_t)-1) && (kr_drand_r(&b->x) > b->s[id].hw[0]))
{
hn = b->s[id].h[1]-1;
}
b->x = kr_splitmix64(b->x);
k = b->x%(b->m[hn].n);
if(b->m[hn].a[k] == b->s[id].s && b->m[hn].n > 1)
{
k = b->x%(b->m[hn].n-1);
if(b->m[hn].a[k] == b->s[id].s) k = b->m[hn].n-1;
}
return b->m[hn].a[k];
}
static void mcgg_perturb(const mc_opt_t *opt, const mc_match_t *ma, mcgg_svaux_t *b)
{
@@ -3448,8 +3461,8 @@ uint32_t mcgg_solve_cc(const mc_opt_t *opt, const mc_gg_t *mg, mcgg_svaux_t *b,
for (j = 0; j < b->cc_size; ++j) back_status(b, b->cc_node[j], 0);
}
fprintf(stderr, "\nBeg-[M::%s::score->%f]\n", __func__, mcgg_score(mg->e, b));
print_mcgg_node(mg->e, b, 3838);
print_mcgg_node(mg->e, b, 36880);
// print_mcgg_node(mg->e, b, 3838);
// print_mcgg_node(mg->e, b, 36880);
// tt0 = tt1 = 0;
for (k = 0; k < (uint32_t)opt->n_perturb; ++k) {
@@ -3458,7 +3471,6 @@ uint32_t mcgg_solve_cc(const mc_opt_t *opt, const mc_gg_t *mg, mcgg_svaux_t *b,
else mcgg_perturb_node(opt, mg->e, b, 3);
// tt0 += yak_realtime()-t0;
// fprintf(stderr, "\n++(%u) sc_pre: %f\n", k, mcgg_score(mg->e, b));
// t1 = yak_realtime();
sc = mcgg_optimize_local(opt, mg->e, b, &n_iter);
// tt1 += yak_realtime()-t1;
@@ -3479,9 +3491,9 @@ uint32_t mcgg_solve_cc(const mc_opt_t *opt, const mc_gg_t *mg, mcgg_svaux_t *b,
for (j = 0; j < b->cc_size; ++j) back_status(b, b->cc_node[j], 1);
sc_opt = sc;
}
fprintf(stderr, "\n");
print_mcgg_node(mg->e, b, 3838);
print_mcgg_node(mg->e, b, 36880);
// fprintf(stderr, "\n");
// print_mcgg_node(mg->e, b, 3838);
// print_mcgg_node(mg->e, b, 36880);
// if((k&31)==0)fprintf(stderr, "+++(%u) sc: %f, sc_opt: %f, tt0: %.3f, tt1: %.3f\n", k, sc, sc_opt, tt0, tt1);
}
@@ -3680,6 +3692,9 @@ void debug_mc_gg_t(const char* fn, uint32_t update_ta, uint32_t convert_mc_g_t)
mc_opt_init(&opt, asm_opt.n_perturb, asm_opt.f_perturb, asm_opt.seed);
mc_g_t *mg = NULL;
mg = to_mc_g_t(ta, s, un);
char *o_file = get_outfile_name(asm_opt.output_file_name);
trans_chain* t_ch = load_hc_trans(o_file);
mb_solve_core(&opt, mg, &(t_ch->k_trans), 1);
mc_solve_core(&opt, mg, NULL);
}
else
@@ -3699,6 +3714,8 @@ void clean_solve_general_ovlp(kv_u_trans_t *ta, uint32_t un, kv_gg_status *s)
void mc_solve_general(kv_u_trans_t *ta, uint32_t un, kv_gg_status *s, uint16_t hapN, uint16_t update_ta, uint16_t write_dump)
{
print_hap_p(s);
exit(1);
mc_opt_t opt;
mc_opt_init(&opt, asm_opt.n_perturb, asm_opt.f_perturb, asm_opt.seed);
mc_gg_t *mg = init_mc_gg_t(un, s, hapN);