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code backup

This commit is contained in:
Heng Li 2014-04-13 12:49:10 -04:00
parent 685cd235a6
commit c9645579bd
1 changed files with 115 additions and 27 deletions
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142
layout.c
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@ -39,7 +39,7 @@ KSORT_INIT(nei, lo_nei_t, nei_lt)
typedef struct { typedef struct {
int id; int id;
int contained:16, marked:16; int contained:16, state:16;
char *name; char *name;
lo_nei_v *nei[2]; lo_nei_v *nei[2];
} vertex_t; } vertex_t;
@ -70,6 +70,12 @@ void lo_opt_init(lo_opt_t *opt)
opt->min_aln_ratio = 0.9; opt->min_aln_ratio = 0.9;
} }
const char *lo_edge_label[] = {
">>", "><", "<>", "<<",
"??", "??", "??", "??",
"C1", "??", "??", "??",
"C2", "??", "??", "??", "IN" };
/********** /**********
* Parser * * Parser *
**********/ **********/
@ -83,6 +89,27 @@ ograph_t *lo_graph_init()
return g; return g;
} }
void lo_print_edge(const ograph_t *g)
{
khint_t k;
for (k = 0; k != kh_end(g->e); ++k) {
if (kh_exist(g->e, k) && !kh_val(g->e, k).reduced) {
int id[2];
edgeinfo_t *e = &kh_val(g->e, k);
id[0] = kh_key(g->e, k)>>32;
id[1] = (uint32_t)kh_key(g->e, k);
if (e->s[1] < e->e[1])
printf("%s\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t%.3f\n", lo_edge_label[e->type],
g->v.a[id[0]].name, e->l[0], e->s[0], e->e[0],
g->v.a[id[1]].name, e->l[1], e->s[1], e->e[1], e->usc);
else
printf("%s\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t%.3f\n", lo_edge_label[e->type],
g->v.a[id[0]].name, e->l[0], e->e[0], e->s[0],
g->v.a[id[1]].name, e->l[1], e->e[1], e->s[1], e->usc);
}
}
}
int lo_infer_edge_type(const lo_opt_t *opt, int l[2], int s[2], int e[2], int d[2]) int lo_infer_edge_type(const lo_opt_t *opt, int l[2], int s[2], int e[2], int d[2])
{ {
int el, x[2], a[2], r[2]; // x: eXtended length, a: Aligned length; r: Remaining length int el, x[2], a[2], r[2]; // x: eXtended length, a: Aligned length; r: Remaining length
@ -132,7 +159,7 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
z = kv_pushp(vertex_t, g->v); z = kv_pushp(vertex_t, g->v);
z->id = kh_size(g->n); z->id = kh_size(g->n);
z->name = strdup(p); z->name = strdup(p);
z->contained = 0; z->contained = z->state = 0;
z->nei[0] = z->nei[1] = 0; // don't initialize the neighbor list right now z->nei[0] = z->nei[1] = 0; // don't initialize the neighbor list right now
k = kh_put(name, g->n, z->name, &absent); k = kh_put(name, g->n, z->name, &absent);
assert(absent); assert(absent);
@ -160,8 +187,13 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
g->v.a[id[1]].contained = 1; g->v.a[id[1]].contained = 1;
} else if (e.type < 4) { // a suffix-prefix overlap } else if (e.type < 4) { // a suffix-prefix overlap
uint64_t x = (uint64_t)id[0]<<32 | id[1]; uint64_t x = (uint64_t)id[0]<<32 | id[1];
int sc_new, sc_old;
edgeinfo_t *f;
k = kh_put(edge, g->e, x, &absent); k = kh_put(edge, g->e, x, &absent);
if (absent || kh_val(g->e, k).usc < e.usc) // TODO: compare the total score, not unit score! f = &kh_val(g->e, k);
sc_old = f->usc * (abs(f->s[0] - f->e[0]) > abs(f->s[1] - f->e[1])? abs(f->s[0] - f->e[0]) : abs(f->s[1] - f->e[1]));
sc_new = e.usc * (abs(e.s[0] - e.e[0]) > abs(e.s[1] - e.e[1])? abs(e.s[0] - e.e[0]) : abs(e.s[1] - e.e[1]));
if (absent || sc_old < sc_new) // TODO: compare the total score, not unit score!
kh_val(g->e, k) = e; kh_val(g->e, k) = e;
} }
// printf("%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id[0], e.l[0], e.s[0], e.e[0], id[1], e.l[1], e.s[1], e.e[1]); // printf("%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id[0], e.l[0], e.s[0], e.e[0], id[1], e.l[1], e.s[1], e.e[1]);
@ -242,6 +274,31 @@ void lo_rm_conflict(ograph_t *g)
{ {
} }
void lo_print_nei(ograph_t *g)
{
int i;
for (i = 0; i < g->v.n; ++i) {
vertex_t *p = &g->v.a[i];
if (p->nei[0]) ks_introsort(nei, p->nei[0]->n, p->nei[0]->a);
if (p->nei[1]) ks_introsort(nei, p->nei[1]->n, p->nei[1]->a);
if (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) {
lo_nei_t *q = &p->nei[j]->a[k];
if (k) putchar(',');
printf("%s%c%d:%c", g->v.a[q->id].name, "<>"[q->ori], q->dist, "+-"[q->reduced]);
}
} else printf("\t*");
}
putchar('\n');
}
}
}
void lo_populate_nei(ograph_t *g) void lo_populate_nei(ograph_t *g)
{ {
int i; int i;
@ -265,34 +322,64 @@ void lo_populate_nei(ograph_t *g)
p = kv_pushp(lo_nei_t, *g->v.a[id[1]].nei[e->type&1]); p = kv_pushp(lo_nei_t, *g->v.a[id[1]].nei[e->type&1]);
p->dist = e->d[1], p->id = id[0], p->ori = e->type>>1^1, p->reduced = 0; p->dist = e->d[1], p->id = id[0], p->ori = e->type>>1^1, p->reduced = 0;
} }
for (i = 0; i < g->v.n; ++i) {
vertex_t *p = &g->v.a[i];
if (p->nei[0]) ks_introsort(nei, p->nei[0]->n, p->nei[0]->a);
if (p->nei[1]) ks_introsort(nei, 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) {
lo_nei_t *q = &p->nei[j]->a[k];
if (k) putchar(',');
printf("%c%s:%d", "+-"[q->ori], g->v.a[q->id].name, q->dist);
}
} else printf("\t*");
}
putchar('\n');
}
}
} }
void lo_trans_reduce(ograph_t *g) static inline edgeinfo_t *lo_get_edge(ehash_t *e, int id0, int id1)
{ {
int i; khint_t k;
k = kh_get(edge, e, (uint64_t)id0<<32 | id1);
return k == kh_end(e)? 0 : &kh_val(e, k);
}
void lo_trans_reduce(ograph_t *g, int fd) // fd: fuzzy distance
{
int i, j, k, l;
for (i = 0; i < g->v.n; ++i)
g->v.a[i].state = 0;
for (i = 0; i < g->v.n; ++i) { for (i = 0; i < g->v.n; ++i) {
vertex_t *p = &g->v.a[i]; vertex_t *pi = &g->v.a[i];
if (pi->nei[0] == 0) continue;
for (j = 0; j < 2; ++j) {
int max;
lo_nei_v *q = pi->nei[j];
if (q->n == 0) continue;
for (k = 0; k < q->n; ++k)
g->v.a[q->a[k].id].state = 1;
max = q->a[q->n - 1].dist + fd;
// loop between line 9--14
for (k = 0; k < q->n; ++k) {
vertex_t *pk = &g->v.a[q->a[k].id];
if (pk->state == 1) {
lo_nei_v *r = pk->nei[q->a[k].ori^1];
for (l = 0; l < r->n && r->a[l].dist + q->a[k].dist < max; ++l)
if (g->v.a[r->a[l].id].state == 1)
g->v.a[r->a[l].id].state = 2;
}
}
// loop between line 20--23
for (k = 0; k < q->n; ++k) {
if (g->v.a[q->a[k].id].state == 2) {
edgeinfo_t *e;
e = lo_get_edge(g->e, i, q->a[k].id);
e->reduced = 1;
e = lo_get_edge(g->e, q->a[k].id, i);
e->reduced = 1;
}
g->v.a[q->a[k].id].state = 0;
}
}
} }
for (i = 0; i < g->v.n; ++i) {
vertex_t *pi = &g->v.a[i];
if (pi->nei[0] == 0) continue;
for (j = 0; j < 2; ++j) {
lo_nei_v *q = pi->nei[j];
for (k = 0; k < q->n; ++k)
q->a[k].reduced = lo_get_edge(g->e, i, q->a[k].id)->reduced;
}
}
if (lo_verbose == 4) lo_print_edge(g);
if (lo_verbose == 5) lo_print_nei(g);
} }
/***************** /*****************
@ -321,7 +408,8 @@ int main_layout(int argc, char *argv[])
lo_rm_contained(g); lo_rm_contained(g);
lo_rm_conflict(g); lo_rm_conflict(g);
lo_populate_nei(g); lo_populate_nei(g);
lo_trans_reduce(g); if (lo_verbose == 6) lo_print_edge(g);
lo_trans_reduce(g, 10);
lo_graph_destroy(g); lo_graph_destroy(g);
ks_destroy(ks); ks_destroy(ks);
gzclose(fp); gzclose(fp);