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r493 ->HiC/UL/Trans

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chhylp123
2023-01-11 20:38:45 -05:00
parent a674110b23
commit 0613b18af9
19 changed files with 3230 additions and 461 deletions
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72
rcut.cpp
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@@ -3241,6 +3241,15 @@ mc_clus_t *init_mc_clus_t(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub, uin
return p;
}
void des_mc_clus_t(mc_clus_t *p)
{
if((!p)) return;
uint32_t k; free(p->lock);
for (k = 0; k < p->n_thread; k++) free(p->aux[k].vis.a);
free(p->aux); free(p->cc.ng.a); free(p->cc.nn.a);
free(p);
}
void mc_solve_core_adv(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub)
{
double index_time = yak_realtime();
@@ -3277,7 +3286,7 @@ void mc_solve_core_adv(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub)
// if(bp) mc_solve_bp(bp);
///mc_write_info(g, b);
mc_svaux_destroy(b);
mc_svaux_destroy(b); des_mc_clus_t(bc);
// if(bp) destroy_mc_bp_t(&bp);
fprintf(stderr, "[M::%s::%.3f] ==> Partition\n", __func__, yak_realtime()-index_time);
}
@@ -4464,6 +4473,28 @@ void dump_bubble_type(bubble_type* bub, FILE *fp)
dump_ma_ug_t(bub->ug, fp);
}
void dump_rid(All_reads *rdb, FILE *fp)
{
fwrite(&(rdb->total_reads), sizeof(rdb->total_reads), 1, fp);
fwrite(&(rdb->name_index_size), sizeof(rdb->name_index_size), 1, fp);
fwrite(rdb->name_index, sizeof((*(rdb->name_index))), rdb->name_index_size, fp);
fwrite(&(rdb->total_name_length), sizeof(rdb->total_name_length), 1, fp);
fwrite(rdb->name, sizeof((*(rdb->name))), rdb->total_name_length, fp);
}
void load_rid(All_reads *rdb, FILE *fp)
{
fread(&(rdb->total_reads), sizeof(rdb->total_reads), 1, fp);
fread(&(rdb->name_index_size), sizeof(rdb->name_index_size), 1, fp);
MALLOC(rdb->name_index, rdb->name_index_size);
fread(rdb->name_index, sizeof((*(rdb->name_index))), rdb->name_index_size, fp);
fread(&(rdb->total_name_length), sizeof(rdb->total_name_length), 1, fp);
MALLOC(rdb->name, rdb->total_name_length);
fread(rdb->name, sizeof((*(rdb->name))), rdb->total_name_length, fp);
}
void dump_debug_phasing(const char* fn, kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g, double f_rate,
uint32_t renew_s, int8_t *s, uint32_t is_sys, bubble_type* bub, kv_u_trans_t *ref)
{
@@ -4481,6 +4512,7 @@ uint32_t renew_s, int8_t *s, uint32_t is_sys, bubble_type* bub, kv_u_trans_t *re
fwrite(&is_sys, sizeof(is_sys), 1, fp);///is_sys
dump_bubble_type(bub, fp);///bub
dump_kv_u_trans_t(ref, fp);///ta
dump_rid(&R_INF, fp);
fclose(fp);
free(buf);
@@ -4586,15 +4618,43 @@ uint32_t *renew_s, int8_t **s, uint32_t *is_sys, bubble_type **bub, kv_u_trans_t
CALLOC((*bub), 1); load_bubble_type(*bub, fp);///bub
CALLOC((*ref), 1); load_kv_u_trans_t(*ref, fp);///ta
load_rid(&R_INF, fp);///read id
fclose(fp);
free(buf);
}
void prt_rcut_res(const char* fn, int8_t *s, ma_ug_t *ug, asg_t *sg)
{
uint32_t i, k, flag = AMBIGU;
char *buf = (char*)calloc(strlen(fn) + 50, 1);
sprintf(buf, "%s.rcut.res.log", fn);
FILE *fp = fopen(buf, "w");
uint8_t *rs = NULL; MALLOC(rs, sg->n_seq);
memset(rs, AMBIGU, sg->n_seq*sizeof((*rs)));
for (i = 0; i < ug->g->n_seq; i++) {
if(ug->g->seq[i].del) continue;
flag = AMBIGU;
if(s[i] == 0) continue;
flag = (s[i] > 0? FATHER:MOTHER);
for (k = 0; k < ug->u.a[i].n; k++) rs[ug->u.a[i].a[k]>>33] = flag;
}
for (i = 0; i < sg->n_seq; i++) {
if(rs[i] == AMBIGU) continue;
fprintf(fp, "%.*s\t%u\n", (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i), rs[i]);
}
fclose(fp); free(rs);
free(buf);
}
void quick_debug_phasing(const char* fn)
{
kv_u_trans_t *ta; ma_ug_t *ug; asg_t *read_g; double f_rate;
uint32_t renew_s; int8_t *s; uint32_t is_sys, k; bubble_type *bub; kv_u_trans_t *ref;
uint32_t renew_s; int8_t *s; uint32_t is_sys; bubble_type *bub; kv_u_trans_t *ref;
load_debug_phasing(fn, &ta, &ug, &read_g, &f_rate, &renew_s, &s, &is_sys, &bub, &ref);
@@ -4602,10 +4662,10 @@ void quick_debug_phasing(const char* fn)
mc_solve(NULL, NULL, ta, ug, read_g, f_rate, NULL, renew_s, s, is_sys, bub, ref, 0, 0);
// mc_solve_core_adv(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub, kv_u_trans_t *ref)
for (k = 0; k < ug->g->n_seq; k++) {
fprintf(stderr, "utg%.6dl(len::%u), s[k]::%d\n", (int32_t)(k)+1, ug->g->seq[k].len, s[k]);
}
// for (k = 0; k < ug->g->n_seq; k++) {
// fprintf(stderr, "utg%.6dl(len::%u), s[k]::%d\n", (int32_t)(k)+1, ug->g->seq[k].len, s[k]);
// }
prt_rcut_res(fn, s, ug, read_g);
exit(1);
}