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code backup

This commit is contained in:
Heng Li 2014-04-09 23:41:39 -04:00
parent bcf6d1b355
commit cf6661a8fe
1 changed files with 21 additions and 19 deletions
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40
layout.c
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@ -11,6 +11,9 @@
#include "kseq.h" #include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 0x10000) KSTREAM_INIT(gzFile, gzread, 0x10000)
#include "ksort.h"
KSORT_INIT_GENERIC(uint64_t)
static int lo_verbose = 3; static int lo_verbose = 3;
/*********************** /***********************
@ -26,14 +29,13 @@ typedef struct {
float min_aln_ratio; float min_aln_ratio;
} lo_opt_t; } lo_opt_t;
KHASH_MAP_INIT_INT(int, int) typedef kvec_t(uint64_t) uint64_v;
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[2]; uint64_v *nei[2];
} vertex_t; } vertex_t;
typedef kvec_t(vertex_t) vertex_v; typedef kvec_t(vertex_t) vertex_v;
@ -122,7 +124,7 @@ 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] = z->nei[1] = 0; // don't initialize the hash table 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);
kh_val(g->n, k) = z->id; kh_val(g->n, k) = z->id;
@ -165,8 +167,8 @@ 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[0]) kh_destroy(int, g->v.a[i].nei[0]); if (g->v.a[i].nei[0]) free(g->v.a[i].nei[0]->a);
if (g->v.a[i].nei[1]) kh_destroy(int, g->v.a[i].nei[1]); if (g->v.a[i].nei[1]) free(g->v.a[i].nei[1]->a);
free(g->v.a[i].name); free(g->v.a[i].name);
} }
free(g->v.a); free(g->v.a);
@ -187,7 +189,7 @@ static inline void lo_flip_edge(edgeinfo_t *e)
lo_swap(tmp, e->l[0], e->l[1]); lo_swap(tmp, e->l[0], e->l[1]);
lo_swap(tmp, e->s[0], e->s[1]); lo_swap(tmp, e->s[0], e->s[1]);
lo_swap(tmp, e->e[0], e->e[1]); lo_swap(tmp, e->e[0], e->e[1]);
e->type = (e->type|1)<<1 | (e->type|2)>>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)
@ -228,27 +230,26 @@ void lo_rm_contained(ograph_t *g)
void lo_populate_nei(ograph_t *g) void lo_populate_nei(ograph_t *g)
{ {
int i, absent; int i;
khint_t k, l; khint_t k;
for (i = 0; i < g->v.n; ++i) { for (i = 0; i < g->v.n; ++i) {
if (g->v.a[i].contained) continue; if (g->v.a[i].contained) continue;
g->v.a[i].nei[0] = kh_init(int); g->v.a[i].nei[0] = calloc(1, sizeof(uint64_v));
g->v.a[i].nei[1] = kh_init(int); g->v.a[i].nei[1] = calloc(1, sizeof(uint64_v));
} }
for (k = 0; k != kh_end(g->e); ++k) { for (k = 0; k != kh_end(g->e); ++k) {
int id[2]; int id[2];
edgeinfo_t *e; edgeinfo_t *e;
vertex_t *v;
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);
e = &kh_val(g->e, k); e = &kh_val(g->e, k);
v = &g->v.a[id[0]]; 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));
l = kh_put(int, v->nei[!(e->type>>1)], id[1]<<1|(e->type&1), &absent); 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));
kh_val(v->nei[!(e->type>>1)], l) = e->d[0]; }
v = &g->v.a[id[1]]; for (i = 0; i < g->v.n; ++i) {
l = kh_put(int, v->nei[e->type&1], id[0]<<1|(e->type>>1^1), &absent); 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);
kh_val(v->nei[e->type&1], l) = e->d[1]; 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);
} }
} }
@ -265,7 +266,8 @@ int main_layout(int argc, char *argv[])
int c; int c;
lo_opt_init(&opt); lo_opt_init(&opt);
while ((c = getopt(argc, argv, "")) >= 0) { while ((c = getopt(argc, argv, "v:")) >= 0) {
if (c == 'v') lo_verbose = atoi(optarg);
} }
if (argc == optind && isatty(fileno(stdin))) { if (argc == optind && isatty(fileno(stdin))) {
fprintf(stderr, "Usage: bwa layout <in.ovlp>\n"); fprintf(stderr, "Usage: bwa layout <in.ovlp>\n");