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fixed a bug in overlap type inferrence

This commit is contained in:
Heng Li 2014-04-11 11:14:06 -04:00
parent bbcabfe342
commit 42e2a7ad46
1 changed files with 12 additions and 6 deletions
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18
layout.c
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@ -33,7 +33,7 @@ typedef kvec_t(uint64_t) uint64_v;
typedef struct {
int id;
int contained;
int contained:16, marked:16;
char *name;
uint64_v *nei[2];
} vertex_t;
@ -41,7 +41,9 @@ typedef struct {
typedef kvec_t(vertex_t) vertex_v;
typedef struct {
int type, score, l[2], s[2], e[2], d[2]; // length, start and end
int type:16, reduced:16;
int l[2], s[2], e[2], d[2]; // length, start and end
float usc;
} edgeinfo_t;
KHASH_MAP_INIT_INT64(edge, edgeinfo_t)
@ -92,12 +94,12 @@ int lo_infer_edge_type(const lo_opt_t *opt, int l[2], int s[2], int e[2], int d[
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 ((double)a[0] / x[0] >= opt->min_aln_ratio && (double)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, 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 = (double)x[0] / l[0] > (double)x[1] / l[1]? LO_T_C1 : LO_T_C2;
} else type = LO_T_I; // internal local match; not a suffix-prefix match
return type;
}
@ -139,7 +141,7 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
else if (i == 5) e.l[1] = strtol(p, &p, 10);
else if (i == 6) e.s[1] = strtol(p, &p, 10);
else if (i == 7) e.e[1] = strtol(p, &p, 10);
else if (i == 8) e.score= strtol(p, &p, 10);
else if (i == 8) e.usc = strtod(p, &p);
++i;
p = q + 1;
if (*q == 0) break;
@ -153,7 +155,7 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
} else if (e.type < 4) { // a suffix-prefix overlap
uint64_t x = (uint64_t)id[0]<<32 | id[1];
k = kh_put(edge, g->e, x, &absent);
if (absent || kh_val(g->e, k).score < e.score)
if (absent || kh_val(g->e, k).usc < e.usc) // TODO: compare the total score, not unit score!
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]);
@ -278,6 +280,10 @@ void lo_populate_nei(ograph_t *g)
void lo_trans_reduce(ograph_t *g)
{
int i;
for (i = 0; i < g->v.n; ++i) {
vertex_t *p = &g->v.a[i];
}
}
/*****************