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code backup

This commit is contained in:
Heng Li 2014-04-09 16:49:37 -04:00
parent 8220008564
commit bcf6d1b355
1 changed files with 78 additions and 12 deletions
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90
layout.c
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@ -4,6 +4,8 @@
#include <stdlib.h> #include <stdlib.h>
#include <stdint.h> #include <stdint.h>
#include <string.h> #include <string.h>
#include <assert.h>
#include "kvec.h" #include "kvec.h"
#include "khash.h" #include "khash.h"
#include "kseq.h" #include "kseq.h"
@ -24,20 +26,20 @@ typedef struct {
float min_aln_ratio; float min_aln_ratio;
} lo_opt_t; } lo_opt_t;
KHASH_SET_INIT_INT(int) KHASH_MAP_INIT_INT(int, int)
typedef khash_t(int) inthash_t; typedef khash_t(int) inthash_t;
typedef struct { typedef struct {
int id; int id;
int contained; int contained;
char *name; char *name;
inthash_t *nei; inthash_t *nei[2];
} vertex_t; } vertex_t;
typedef kvec_t(vertex_t) vertex_v; typedef kvec_t(vertex_t) vertex_v;
typedef struct { typedef struct {
int type, score, l[2], s[2], e[2]; // length, start and end int type, score, l[2], s[2], e[2], d[2]; // length, start and end
} edgeinfo_t; } edgeinfo_t;
KHASH_MAP_INIT_INT64(edge, edgeinfo_t) KHASH_MAP_INIT_INT64(edge, edgeinfo_t)
@ -71,7 +73,7 @@ ograph_t *lo_graph_init()
return g; return g;
} }
int lo_infer_edge_type(const lo_opt_t *opt, int l[2], int s[2], int e[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
int t[2][2], type; int t[2][2], type;
@ -93,6 +95,7 @@ int lo_infer_edge_type(const lo_opt_t *opt, int l[2], int s[2], int e[2])
if (r[0] < 0) type ^= 3; // reverse the direction if (r[0] < 0) type ^= 3; // reverse the direction
} else type = x[0] / l[0] > x[1] / l[1]? LO_T_C1 : LO_T_C2; } 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 } 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; return type;
} }
@ -119,8 +122,9 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
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 = 0;
z->nei = 0; // don't initialize the hash table right now z->nei[0] = z->nei[1] = 0; // don't initialize the hash table right now
k = kh_put(name, g->n, z->name, &absent); k = kh_put(name, g->n, z->name, &absent);
assert(absent);
kh_val(g->n, k) = z->id; kh_val(g->n, k) = z->id;
} }
id[(i==4)] = kh_val(g->n, k); id[(i==4)] = kh_val(g->n, k);
@ -138,7 +142,7 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
if (*q == 0) break; if (*q == 0) break;
} }
if (i < 9) continue; // not enough fields if (i < 9) continue; // not enough fields
e.type = lo_infer_edge_type(opt, e.l, e.s, e.e); e.type = lo_infer_edge_type(opt, e.l, e.s, e.e, e.d);
if (e.type == LO_T_C1) { if (e.type == LO_T_C1) {
g->v.a[id[0]].contained = 1; g->v.a[id[0]].contained = 1;
} else if (e.type == LO_T_C2) { } else if (e.type == LO_T_C2) {
@ -152,7 +156,8 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
// 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]);
} }
free(str.s); free(str.s);
if (lo_verbose >= 3) fprintf(stderr, "[M::%s] read %d edges\n", __func__, kh_size(g->e)); if (lo_verbose >= 3)
fprintf(stderr, "[M::%s] read %d edges\n", __func__, kh_size(g->e));
return g; return g;
} }
@ -160,7 +165,8 @@ void lo_graph_destroy(ograph_t *g)
{ {
int i; int i;
for (i = 0; i < g->v.n; ++i) { for (i = 0; i < g->v.n; ++i) {
if (g->v.a[i].nei) kh_destroy(int, g->v.a[i].nei); if (g->v.a[i].nei[0]) kh_destroy(int, g->v.a[i].nei[0]);
if (g->v.a[i].nei[1]) kh_destroy(int, g->v.a[i].nei[1]);
free(g->v.a[i].name); free(g->v.a[i].name);
} }
free(g->v.a); free(g->v.a);
@ -173,18 +179,77 @@ void lo_graph_destroy(ograph_t *g)
* Graph routines * * Graph routines *
******************/ ******************/
#define lo_swap(tmp, a, b) ((tmp) = (a), (a) = (b), (b) = (tmp))
static inline void lo_flip_edge(edgeinfo_t *e)
{
int tmp;
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;
}
void lo_rm_contained(ograph_t *g) void lo_rm_contained(ograph_t *g)
{ {
khint_t k; khint_t k, l;
int n_del = 0, n_add = 0, absent;
ehash_t *tmp;
tmp = kh_init(edge);
for (k = 0; k != kh_end(g->e); ++k) { for (k = 0; k != kh_end(g->e); ++k) {
int id[2]; int id[2];
if (!kh_exist(g->e, k)) continue; if (!kh_exist(g->e, k)) continue;
id[0] = kh_key(g->e, k)>>32; id[0] = kh_key(g->e, k)>>32;
id[1] = (uint32_t)kh_key(g->e, k); id[1] = (uint32_t)kh_key(g->e, k);
if (g->v.a[id[0]].contained || g->v.a[id[1]].contained) if (g->v.a[id[0]].contained || g->v.a[id[1]].contained) {
kh_del(edge, g->e, k); ++n_del;
kh_del(edge, g->e, k); // kh_del() will not trigger rehash
} else {
uint64_t key2 = (uint64_t)id[1]<<32|id[0];
l = kh_get(edge, g->e, key2);
if (l == kh_end(g->e)) {
l = kh_put(edge, tmp, key2, &absent);
kh_val(tmp, l) = kh_val(g->e, k);
lo_flip_edge(&kh_val(tmp, l));
++n_add;
}
}
}
for (k = 0; k != kh_end(tmp); ++k) {
if (!kh_exist(tmp, k)) continue;
l = kh_put(edge, g->e, kh_key(tmp, k), &absent);
assert(absent);
kh_val(g->e, l) = kh_val(tmp, k);
}
if (lo_verbose >= 3)
fprintf(stderr, "[M::%s] removed %d and added %d; %d edges remain\n", __func__, n_del, kh_size(tmp), kh_size(g->e));
kh_destroy(edge, tmp);
}
void lo_populate_nei(ograph_t *g)
{
int i, absent;
khint_t k, l;
for (i = 0; i < g->v.n; ++i) {
if (g->v.a[i].contained) continue;
g->v.a[i].nei[0] = kh_init(int);
g->v.a[i].nei[1] = kh_init(int);
}
for (k = 0; k != kh_end(g->e); ++k) {
int id[2];
edgeinfo_t *e;
vertex_t *v;
if (!kh_exist(g->e, k)) continue;
id[0] = kh_key(g->e, k)>>32;
id[1] = (uint32_t)kh_key(g->e, k);
e = &kh_val(g->e, k);
v = &g->v.a[id[0]];
l = kh_put(int, v->nei[!(e->type>>1)], id[1]<<1|(e->type&1), &absent);
kh_val(v->nei[!(e->type>>1)], l) = e->d[0];
v = &g->v.a[id[1]];
l = kh_put(int, v->nei[e->type&1], id[0]<<1|(e->type>>1^1), &absent);
kh_val(v->nei[e->type&1], l) = e->d[1];
} }
if (lo_verbose >= 3) fprintf(stderr, "[M::%s] %d edges remain after removing contained vertices\n", __func__, kh_size(g->e));
} }
/***************** /*****************
@ -210,6 +275,7 @@ int main_layout(int argc, char *argv[])
ks = ks_init(fp); ks = ks_init(fp);
g = lo_graph_parse(&opt, ks); g = lo_graph_parse(&opt, ks);
lo_rm_contained(g); lo_rm_contained(g);
lo_populate_nei(g);
lo_graph_destroy(g); lo_graph_destroy(g);
ks_destroy(ks); ks_destroy(ks);
gzclose(fp); gzclose(fp);