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code backup

This commit is contained in:
Heng Li 2014-04-10 10:34:57 -04:00
parent cf6661a8fe
commit 22c1d3cecc
1 changed files with 34 additions and 5 deletions
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39
layout.c
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@ -91,13 +91,14 @@ int lo_infer_edge_type(const lo_opt_t *opt, int l[2], int s[2], int e[2], int d[
el = r[0] < 0? t[0][0] : t[0][1];
el += r[1] < 0? t[1][1] : t[1][0];
x[0] += el, x[1] += el;
d[0] = d[1] = -1;
if ((float)a[0] / x[0] >= opt->min_aln_ratio && (float)a[1] / x[1] >= opt->min_aln_ratio) {
if ((r[0] >= opt->min_ext && r[1] >= opt->min_ext) || (r[0] <= -opt->min_ext && r[1] <= -opt->min_ext)) { // suffix-prefix match
type = s[0] < e[0]? 0 : 2;
if (r[0] < 0) type ^= 3; // reverse the direction
if (r[0] < 0) type ^= 3, d[0] = -r[1], d[1] = -r[0]; // reverse the direction
else d[0] = r[0], d[1] = r[1];
} else type = x[0] / l[0] > x[1] / l[1]? LO_T_C1 : LO_T_C2;
} else type = LO_T_I; // internal local match; not a suffix-prefix match
d[0] = abs(r[0]); d[1] = abs(r[1]);
return type;
}
@ -189,7 +190,8 @@ static inline void lo_flip_edge(edgeinfo_t *e)
lo_swap(tmp, e->l[0], e->l[1]);
lo_swap(tmp, e->s[0], e->s[1]);
lo_swap(tmp, e->e[0], e->e[1]);
e->type = (e->type&1)<<1 | (e->type&2)>>1;
lo_swap(tmp, e->d[0], e->d[1]);
e->type = ((e->type&1)<<1 | (e->type&2)>>1) ^ 3;
}
void lo_rm_contained(ograph_t *g)
@ -228,6 +230,10 @@ void lo_rm_contained(ograph_t *g)
kh_destroy(edge, tmp);
}
void lo_rm_conflict(ograph_t *g)
{
}
void lo_populate_nei(ograph_t *g)
{
int i;
@ -243,16 +249,37 @@ void lo_populate_nei(ograph_t *g)
if (!kh_exist(g->e, k)) continue;
id[0] = kh_key(g->e, k)>>32;
id[1] = (uint32_t)kh_key(g->e, k);
if (id[0] > id[1]) continue;
e = &kh_val(g->e, k);
kv_push(uint64_t, *g->v.a[id[0]].nei[e->type>>1^1], (uint64_t)e->d[0]<<32 | id[1]<<1 | (e->type&1));
kv_push(uint64_t, *g->v.a[id[1]].nei[e->type&1], (uint64_t)e->d[1]<<32 | id[0]<<1 | (e->type>>1^1));
}
for (i = 0; i < g->v.n; ++i) {
if (g->v.a[i].nei[0]) ks_introsort(uint64_t, g->v.a[i].nei[0]->n, g->v.a[i].nei[0]->a);
if (g->v.a[i].nei[1]) ks_introsort(uint64_t, g->v.a[i].nei[1]->n, g->v.a[i].nei[1]->a);
vertex_t *p = &g->v.a[i];
if (p->nei[0]) ks_introsort(uint64_t, p->nei[0]->n, p->nei[0]->a);
if (p->nei[1]) ks_introsort(uint64_t, p->nei[1]->n, p->nei[1]->a);
if (lo_verbose >= 4 && p->nei[0]) {
int j, k;
printf("%s\t%ld,%ld", p->name, p->nei[0]->n, p->nei[1]->n);
for (j = 0; j < 2; ++j) {
if (p->nei[j]->n) {
putchar('\t');
for (k = 0; k < p->nei[j]->n; ++k) {
uint64_t x = p->nei[j]->a[k];
if (k) putchar(',');
printf("%c%s:%d", "+-"[x&1], g->v.a[((uint32_t)x)>>1].name, (uint32_t)(x>>32));
}
} else printf("\t*");
}
putchar('\n');
}
}
}
void lo_trans_reduce(ograph_t *g)
{
}
/*****************
* Main function *
*****************/
@ -277,7 +304,9 @@ int main_layout(int argc, char *argv[])
ks = ks_init(fp);
g = lo_graph_parse(&opt, ks);
lo_rm_contained(g);
lo_rm_conflict(g);
lo_populate_nei(g);
lo_trans_reduce(g);
lo_graph_destroy(g);
ks_destroy(ks);
gzclose(fp);