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chhylp123
2020-10-19 19:51:17 -04:00
parent b1f844801a
commit 04f94514ee
1 changed files with 65 additions and 9 deletions
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Overlaps.cpp
+65 -9
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@@ -9464,8 +9464,8 @@ ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
if(u->m == 0) continue;
polish_unitig(u, read_g, sources, coverage_cut, edge, max_hang, min_ovlp);
polish_unitig_advance(u, read_g, RNF, sources, coverage_cut, edge, &g_read, &tmp, max_hang, min_ovlp);
g->g->seq[i].len = u->len;
uint32_t l = 0;
u->s = (char*)calloc(1, u->len + 1);
@@ -9514,6 +9514,25 @@ ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
destory_UC_Read(&g_read);
destory_UC_Read(&tmp);
uint32_t n_vtx = g->g->n_seq * 2, v, nv;
uint32_t vLen = 0;
asg_arc_t* av = NULL;
for (v = 0; v < n_vtx; ++v)
{
if (g->g->seq[v>>1].del) continue;
av = asg_arc_a(g->g, v);
nv = asg_arc_n(g->g, v);
for (i = 0; i < nv; i++)
{
if(av[i].del) continue;
vLen = g->g->seq[(av[i].ul>>33)].len - av[i].ol;
av[i].ul = (av[i].ul>>32)<<32;
av[i].ul = av[i].ul | vLen;
}
}
return 0;
}
@@ -9597,12 +9616,48 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FIL
}
}
for (i = 0; i < ug->g->n_arc; ++i) { // the Link lines in GFA
uint32_t u = ug->g->arc[i].ul>>32, v = ug->g->arc[i].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\n",
prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], ug->g->arc[i].ol, asg_arc_len(ug->g->arc[i]));
}
// for (i = 0; i < ug->g->n_arc; ++i) { // the Link lines in GFA
// uint32_t u = ug->g->arc[i].ul>>32, v = ug->g->arc[i].v;
// fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\n",
// prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
// prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], ug->g->arc[i].ol, asg_arc_len(ug->g->arc[i]));
// }
asg_arc_t* au = NULL;
uint32_t nu, u, v;
for (i = 0; i < ug->u.n; ++i) {
if(ug->u.a[i].m == 0) continue;
if(ug->u.a[i].circ)
{
fprintf(fp, "L\t%s%.6dc\t+\t%s%.6dc\t+\t%dM\tL1:i:%d\n",
prefix, i+1, prefix, i+1, 0, ug->u.a[i].len);
fprintf(fp, "L\t%s%.6dc\t-\t%s%.6dc\t-\t%dM\tL1:i:%d\n",
prefix, i+1, prefix, i+1, 0, ug->u.a[i].len);
}
u = i<<1;
au = asg_arc_a(ug->g, u);
nu = asg_arc_n(ug->g, u);
for (j = 0; j < nu; j++)
{
if(au[j].del) continue;
v = au[j].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\n",
prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], au[j].ol, asg_arc_len(au[j]));
}
u = (i<<1) + 1;
au = asg_arc_a(ug->g, u);
nu = asg_arc_n(ug->g, u);
for (j = 0; j < nu; j++)
{
if(au[j].del) continue;
v = au[j].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\n",
prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], au[j].ol, asg_arc_len(au[j]));
}
}
free(primary_flag);
}
@@ -22655,6 +22710,8 @@ void append_utg(ma_ug_t* ptg, ma_ug_t* atg)
ptg->u.n++;
}
if(ptg->g->idx != 0) free(ptg->g->idx);
ptg->g->idx = 0;
asg_cleanup(ptg->g);
}
@@ -22782,7 +22839,6 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex)
asg_symm(nsg);
append_utg(*ptg, atg);
n_vtx = read_g->n_seq;
for (v = 0; v < n_vtx; v++)
{
@@ -26895,6 +26951,7 @@ int max_hang, int min_ovlp)
}
}
void clean_graph(
int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
@@ -27075,7 +27132,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
debug_gfa:;
/*******************************for debug***************************************/
}
/**
debug_ma_hit_t(sources, coverage_cut, n_read, max_hang_length,
mini_overlap_length);