xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-05 05:48:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

cuttoff before debugging

Browse Source
This commit is contained in:
chhylp123
2022-11-05 09:03:23 -04:00
parent e66c003b65
commit 612c1ab712
8 changed files with 1115 additions and 93 deletions
Download Patch File Download Diff File Expand all files Collapse all files
gfa_ut.cpp
+57 -2
View File
@@ -2352,6 +2352,48 @@ void des_flex_asg_t(flex_asg_t *z)
free(z->idx); free(z->pi.a); free(z->a);
}
void print_raw_u2rgfa_seq(all_ul_t *aln, R_to_U* rI, uint32_t is_detail)
{
uint64_t id, a_n, k, z; uc_block_t *a = NULL;
kvec_t(uint8_t) ff; kv_init(ff);
for (id = 0; id < aln->n; id++) {
a = aln->a[id].bb.a; a_n = aln->a[id].bb.n;
if(a_n == 0) continue;
fprintf(stderr,"\n%.*s\tid::%lu\trlen::%u", (int32_t)aln->nid.a[id].n, aln->nid.a[id].a, id, aln->a[id].rlen);
kv_resize(uint8_t, ff, a_n); memset(ff.a, 0, a_n*sizeof((*(ff.a))));
if(is_detail) {
fprintf(stderr, "\n");
for (k = 0; k < a_n; k++) {
if(ff.a[k]) continue;
for (z = k; z != (uint32_t)-1; z = a[z].aidx) {
fprintf(stderr, "%.*s\t%c\tq::[%u, %u)\tt::[%u, %u)\tid::%u\ttl::%lu\tc::%u\n",
(int)Get_NAME_LENGTH(R_INF, a[z].hid), Get_NAME(R_INF, a[z].hid), "+-"[a[z].rev],
a[z].qs, a[z].qe, a[z].ts, a[z].te, a[z].hid, Get_READ_LENGTH(R_INF, a[z].hid),
rI?is_contain_r((*rI), a[z].hid):0);
assert(ff.a[z] == 0);
ff.a[z] = 1;
}
fprintf(stderr, "************\n");
}
} else {
fprintf(stderr, "\t");
for (k = 0; k < a_n; k++) {
if(ff.a[k]) continue;
for (z = k; z != (uint32_t)-1; z = a[z].aidx) {
fprintf(stderr, "%.*s\t",
(int)Get_NAME_LENGTH(R_INF, a[z].hid), Get_NAME(R_INF, a[z].hid));
assert(ff.a[z] == 0);
ff.a[z] = 1;
}
fprintf(stderr, "\n");
}
}
}
kv_destroy(ff);
}
void ul_clean_gfa(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, int64_t clean_round, double min_ovlp_drop_ratio, double max_ovlp_drop_ratio,
double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, int32_t is_ou, int32_t is_trio, uint32_t ou_thres, char *o_file)
{
@@ -2367,7 +2409,20 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
// if(is_ou) update_sg_uo(sg, src);///do not do it here
// print_debug_gfa(sg, NULL, uopt->coverage_cut, "UL.dirty.debug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 1, 0, 0);
// exit(1);
// print_raw_u2rgfa_seq(&UL_INF, rI, 1);
// exit(1);
// fprintf(stderr, "%.*s\tid::%u\tis_c::%u\n",
// (int)Get_NAME_LENGTH(R_INF, 10785), Get_NAME(R_INF, 10785), 10785, is_contain_r((*rI), 10785));
// fprintf(stderr, "%.*s\tid::%u\tis_c::%u\n",
// (int)Get_NAME_LENGTH(R_INF, 10790), Get_NAME(R_INF, 10790), 10790, is_contain_r((*rI), 10790));
// fprintf(stderr, "%.*s\tid::%u\tis_c::%u\n",
// (int)Get_NAME_LENGTH(R_INF, 10805), Get_NAME(R_INF, 10805), 10805, is_contain_r((*rI), 10805));
// fprintf(stderr, "%.*s\tid::%u\tis_c::%u\n",
// (int)Get_NAME_LENGTH(R_INF, 10809), Get_NAME(R_INF, 10809), 10809, is_contain_r((*rI), 10809));
// fprintf(stderr, "%.*s\tid::%u\tis_c::%u\n",
// (int)Get_NAME_LENGTH(R_INF, 10819), Get_NAME(R_INF, 10819), 10819, is_contain_r((*rI), 10819));
// debug_info_of_specfic_node("m64012_190921_234837/111673711/ccs", sg, rI, "beg");
// debug_info_of_specfic_node("m64011_190830_220126/95028102/ccs", sg, rI, "beg");
@@ -11794,7 +11849,7 @@ void u2g_hybrid_clean(ul_resolve_t *uidx, ulg_opt_t *ulopt, usg_t *ng, asg64_v *
debug_sysm_usg_t(ng, __func__);
/******for debug******/
prt_usg_t(uidx, ng, "ng1");
// prt_usg_t(uidx, ng, "ng1");
/******for debug******/
// u2g_hybrid_extend(ng, NULL, b, ub);
@@ -11994,7 +12049,7 @@ void u2g_threading(ul_resolve_t *uidx, ulg_opt_t *ulopt, uint64_t cov_cutoff, as
idx->h_usg = ng;
/******for debug******/
prt_usg_t(uidx, ng, "ng0");
// prt_usg_t(uidx, ng, "ng0");
/******for debug******/