code backup
This commit is contained in:
Heng Li
parent
d5877ad0a9
commit
1209f161c9
2
Makefile
2
Makefile
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@ -1,6 +1,6 @@
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CC= gcc
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#CC= clang --analyze
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CFLAGS= -g -Wall -O2 -Wno-unused-function
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CFLAGS= -g -Wall -Wno-unused-function -O2
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WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
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AR= ar
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DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
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110
layout.c
110
layout.c
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@ -24,6 +24,7 @@ static int lo_verbose = 3;
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typedef struct {
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int min_ext, fuzzy_dist;
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int min_n_ovlp;
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float min_aln_ratio;
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} lo_opt_t;
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@ -37,15 +38,20 @@ typedef kvec_t(lo_nei_t) lo_nei_v;
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#define nei_lt(a, b) ((a).dist < (b).dist)
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KSORT_INIT(nei, lo_nei_t, nei_lt)
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#define LO_VF_CONTAINED 0x1
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#define LO_VF_LACK_OVLP 0x2
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typedef struct {
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int id;
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int contained:16, state:16;
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int flag:16, state:16;
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char *name;
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lo_nei_v *nei[2];
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} vertex_t;
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typedef kvec_t(vertex_t) vertex_v;
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#define lo_skipped(v) ((v)->flag & (LO_VF_CONTAINED|LO_VF_LACK_OVLP))
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typedef struct {
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int type:16, reduced:16;
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int l[2], s[2], e[2], d[2]; // length, start and end
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@ -68,7 +74,8 @@ void lo_opt_init(lo_opt_t *opt)
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{
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opt->min_ext = 50;
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opt->min_aln_ratio = 0.9;
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opt->fuzzy_dist = 500;
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opt->min_n_ovlp = 1;
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opt->fuzzy_dist = 100;
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}
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const char *lo_edge_label[] = {
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@ -160,7 +167,7 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
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z = kv_pushp(vertex_t, g->v);
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z->id = kh_size(g->n);
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z->name = strdup(p);
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z->contained = z->state = 0;
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z->flag = z->state = 0;
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z->nei[0] = z->nei[1] = 0; // don't initialize the neighbor list right now
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k = kh_put(name, g->n, z->name, &absent);
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assert(absent);
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@ -183,9 +190,9 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
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if (i < 9) continue; // not enough fields
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e.type = lo_infer_edge_type(opt, e.l, e.s, e.e, e.d);
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if (e.type == LO_T_C1) {
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g->v.a[id[0]].contained = 1;
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g->v.a[id[0]].flag |= LO_VF_CONTAINED;
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} else if (e.type == LO_T_C2) {
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g->v.a[id[1]].contained = 1;
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g->v.a[id[1]].flag |= LO_VF_CONTAINED;
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} else if (e.type < 4) { // a suffix-prefix overlap
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uint64_t x = (uint64_t)id[0]<<32 | id[1];
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int sc_new, sc_old;
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@ -197,7 +204,6 @@ ograph_t *lo_graph_parse(const lo_opt_t *opt, kstream_t *ks)
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if (absent || sc_old < sc_new) // TODO: compare the total score, not unit score!
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kh_val(g->e, k) = e;
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}
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// 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]);
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}
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free(str.s);
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if (lo_verbose >= 3)
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@ -235,52 +241,88 @@ static inline void lo_flip_edge(edgeinfo_t *e)
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e->type = ((e->type&1)<<1 | (e->type&2)>>1) ^ 3;
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}
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void lo_rm_contained(ograph_t *g)
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void lo_add_missing(ograph_t *g)
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{
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khint_t k, l;
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int n_del = 0, n_add = 0, absent;
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ehash_t *tmp;
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tmp = kh_init(edge);
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int absent;
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ehash_t *added;
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added = kh_init(edge);
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for (k = 0; k != kh_end(g->e); ++k) {
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int id[2];
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if (!kh_exist(g->e, k)) continue;
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id[0] = kh_key(g->e, k)>>32;
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id[1] = (uint32_t)kh_key(g->e, k);
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if (g->v.a[id[0]].contained || g->v.a[id[1]].contained) {
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++n_del;
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kh_del(edge, g->e, k); // kh_del() will not trigger rehash
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} else {
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if (!lo_skipped(&g->v.a[id[0]]) && !lo_skipped(&g->v.a[id[1]])) {
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uint64_t key2 = (uint64_t)id[1]<<32|id[0];
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l = kh_get(edge, g->e, key2);
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if (l == kh_end(g->e)) {
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l = kh_put(edge, tmp, key2, &absent);
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kh_val(tmp, l) = kh_val(g->e, k);
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lo_flip_edge(&kh_val(tmp, l));
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++n_add;
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l = kh_put(edge, added, key2, &absent);
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kh_val(added, l) = kh_val(g->e, k);
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lo_flip_edge(&kh_val(added, l));
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}
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}
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}
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for (k = 0; k != kh_end(tmp); ++k) {
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if (!kh_exist(tmp, k)) continue;
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l = kh_put(edge, g->e, kh_key(tmp, k), &absent);
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for (k = 0; k != kh_end(added); ++k) {
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if (!kh_exist(added, k)) continue;
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l = kh_put(edge, g->e, kh_key(added, k), &absent);
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assert(absent);
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kh_val(g->e, l) = kh_val(tmp, k);
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kh_val(g->e, l) = kh_val(added, k);
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}
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if (lo_verbose >= 3)
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fprintf(stderr, "[M::%s] removed %d and added %d; %d edges remain\n", __func__, n_del, kh_size(tmp), kh_size(g->e));
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kh_destroy(edge, tmp);
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fprintf(stderr, "[M::%s] added %d missing edges. %d edges remain in total.\n", __func__, kh_size(added), kh_size(g->e));
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kh_destroy(edge, added);
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}
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void lo_rm_skipped(ograph_t *g)
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{
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khint_t k;
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int n_del = 0;
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for (k = 0; k != kh_end(g->e); ++k) {
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int id[2];
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if (!kh_exist(g->e, k)) continue;
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id[0] = kh_key(g->e, k)>>32;
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id[1] = (uint32_t)kh_key(g->e, k);
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if (lo_skipped(&g->v.a[id[0]]) || lo_skipped(&g->v.a[id[1]])) {
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++n_del;
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kh_del(edge, g->e, k); // kh_del() will not trigger rehash
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}
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}
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if (lo_verbose >= 3)
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fprintf(stderr, "[M::%s] removed %d edges; %d remain\n", __func__, n_del, kh_size(g->e));
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}
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void lo_rm_conflict(ograph_t *g)
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{
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}
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void lo_mark_lack_ovlp(ograph_t *g, int min_n_ovlp) // can only be called before lo_populate_nei()
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{
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int *count, i, n_marked = 0;
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khint_t k;
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count = calloc(g->v.n<<1, sizeof(int));
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for (k = 0; k != kh_end(g->e); ++k) {
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int id[2];
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edgeinfo_t *e;
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if (!kh_exist(g->e, k) || kh_val(g->e, k).type >= 4) continue;
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e = &kh_val(g->e, k);
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id[0] = kh_key(g->e, k)>>32;
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id[1] = (uint32_t)kh_key(g->e, k);
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++count[id[0]<<1|(e->type>>1^1)];
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++count[id[1]|(e->type&1)];
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}
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for (i = 0; i < g->v.n; ++i)
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if (!lo_skipped(&g->v.a[i]) && (count[i<<1|0] < min_n_ovlp || count[i<<1|1] < min_n_ovlp))
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g->v.a[i].flag |= LO_VF_LACK_OVLP, ++n_marked;
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free(count);
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if (lo_verbose >= 3) fprintf(stderr, "[M::%s] %d vertices to be dropped due to lack of overlaps\n", __func__, n_marked);
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}
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void lo_print_nei(ograph_t *g)
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{
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int i;
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for (i = 0; i < g->v.n; ++i) {
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vertex_t *p = &g->v.a[i];
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if (p->nei[0]) {
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if (!lo_skipped(p) && p->nei[0]) {
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int j, k;
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printf("%s\t%ld,%ld", p->name, p->nei[0]->n, p->nei[1]->n);
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for (j = 0; j < 2; ++j) {
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@ -303,7 +345,7 @@ void lo_populate_nei(ograph_t *g)
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int i;
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khint_t k;
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for (i = 0; i < g->v.n; ++i) {
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if (g->v.a[i].contained) continue;
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if (lo_skipped(&g->v.a[i])) continue;
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g->v.a[i].nei[0] = calloc(1, sizeof(lo_nei_v));
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g->v.a[i].nei[1] = calloc(1, sizeof(lo_nei_v));
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}
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@ -343,7 +385,6 @@ void lo_trans_reduce(ograph_t *g, int fd) // fd: fuzzy distance
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for (i = 0; i < g->v.n; ++i) {
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vertex_t *pi = &g->v.a[i];
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if (pi->nei[0] == 0) continue;
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//printf("===> vertex %s <===\n", pi->name);
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for (j = 0; j < 2; ++j) {
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int max;
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lo_nei_v *q = pi->nei[j];
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@ -351,18 +392,11 @@ void lo_trans_reduce(ograph_t *g, int fd) // fd: fuzzy distance
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for (k = 0; k < q->n; ++k)
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g->v.a[q->a[k].id].state = 1;
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max = q->a[q->n - 1].dist + fd;
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//printf("* max[%c]=%d, %ld, %d\n", "<>"[j], max, q->n, q->a[q->n - 1].dist);
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// loop between line 9--14
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for (k = 0; k < q->n; ++k) {
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vertex_t *pk = &g->v.a[q->a[k].id];
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if (pk->state == 1) {
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lo_nei_v *r = pk->nei[q->a[k].ori^1];
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/*
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printf("** %s: ", pk->name);
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for (l = 0; l < r->n; ++l)
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printf("%s,%d", g->v.a[r->a[k].id].name, r->a[l].dist + q->a[k].dist);
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printf("\n");
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*/
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for (l = 0; l < r->n; ++l)
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if (r->a[l].dist + q->a[k].dist < max && g->v.a[r->a[l].id].state == 1)
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g->v.a[r->a[l].id].state = 2;
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@ -407,9 +441,10 @@ int main_layout(int argc, char *argv[])
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int c;
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lo_opt_init(&opt);
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while ((c = getopt(argc, argv, "v:d:")) >= 0) {
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while ((c = getopt(argc, argv, "v:d:o:")) >= 0) {
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if (c == 'v') lo_verbose = atoi(optarg);
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else if (c == 'd') opt.fuzzy_dist = atoi(optarg);
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else if (c == 'o') opt.min_n_ovlp = atoi(optarg);
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}
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if (argc == optind && isatty(fileno(stdin))) {
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fprintf(stderr, "Usage: bwa layout <in.ovlp>\n");
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@ -418,8 +453,11 @@ int main_layout(int argc, char *argv[])
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fp = (optind == argc && !isatty(fileno(stdin))) || strcmp(argv[optind], "-") == 0? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
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ks = ks_init(fp);
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g = lo_graph_parse(&opt, ks);
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lo_rm_contained(g);
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lo_rm_skipped(g);
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lo_add_missing(g);
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lo_rm_conflict(g);
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lo_mark_lack_ovlp(g, opt.min_n_ovlp);
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lo_rm_skipped(g);
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lo_populate_nei(g);
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if (lo_verbose == 6) lo_print_edge(g);
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lo_trans_reduce(g, opt.fuzzy_dist);
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