mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-01 01:18:13 +08:00
before contain keeping
This commit is contained in:
chhylp123
+1
-1
@@ -4,7 +4,7 @@
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#include <pthread.h>
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#include <stdint.h>
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#define HA_VERSION "0.16.5-r412"
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#define HA_VERSION "0.16.5-r413"
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#define VERBOSE 0
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+165
-50
@@ -6959,7 +6959,7 @@ static inline void ulg_seq_del(ma_ug_t *ug, uint32_t s)
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}
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uint32_t ulg_arc_cut_tips(ul_resolve_t *uidx, ma_ug_t *ug, uint32_t max_ext, uint32_t max_ext_hifi, asg64_v *in, asg64_v *ib)
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uint32_t ulg_arc_cut_tips(ul_resolve_t *uidx, ma_ug_t *ug, uint32_t max_ext, uint32_t max_ext_hifi, uint32_t is_double_check, asg64_v *in, asg64_v *ib)
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{
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asg64_v tx = {0,0,0}, tb = {0,0,0}, *b = NULL, *ub = NULL; asg_t *g = ug->g;
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uint32_t n_vtx = g->n_seq<<1, v, w, i, k, cnt = 0, nv, kv, pb, w_occ, a_occ, ul_occ, del_occ;
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@@ -7016,8 +7016,8 @@ uint32_t ulg_arc_cut_tips(ul_resolve_t *uidx, ma_ug_t *ug, uint32_t max_ext, uin
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if(kv <= max_ext && get_remove_hifi_occ(uidx, max_ext_hifi, b->a + pb, b->n - pb, ub, &del_occ)) {
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// fprintf(stderr, "*[M::%s::] k::%u, v>>1::%u, v&1::%u, kv::%u, max_ext::%u, max_ext_hifi::%u\n\n",
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// __func__, k, v>>1, v&1, kv, max_ext, max_ext_hifi);
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get_bridges(uidx, b->a + pb, b->n - pb, &w_occ, &a_occ);
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if(w_occ > 0 || a_occ > 0 || kv == 0 || del_occ == 0) {
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if(is_double_check) get_bridges(uidx, b->a + pb, b->n - pb, &w_occ, &a_occ);
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if(is_double_check == 0 || w_occ > 0 || a_occ > 0 || kv == 0 || del_occ == 0) {
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for (i = pb; i < b->n; i++) ulg_seq_del(ug, (b->a[i]>>1));
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cnt += b->n - pb;
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}
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@@ -8339,55 +8339,124 @@ uint32_t ul_occ_check(ul_resolve_t *uidx, ma_ug_t *ug, uint32_t qocc_ul, uint32_
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return 0;
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}
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uint32_t idx_check_rate(uint64_t *a, uint64_t a_n, uint64_t tot, uint64_t winlen, float match_rate)
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{
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if(a_n == 0) return 0;
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if(tot < winlen) winlen = tot;
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uint64_t k, mm = a[0]>>32, ks, s, e; int64_t p;
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s = 0; e = winlen;
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for (k = ks = 0; k < a_n; k++) {
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assert(a[k] != (uint64_t)-1);
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// if(mm != (a[k]>>32)) {
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// fprintf(stderr, "***[M::%s::] mm::%lu, (a[%lu]>>32)::%lu\n",
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// __func__, mm, k, (a[k]>>32));
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// }
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assert(mm == (a[k]>>32));
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if(((uint32_t)a[k]) >= s && ((uint32_t)a[k]) < e) continue;
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break;
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}
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p = k;
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if(p > 0 && p >= (int64_t)(winlen*match_rate)) return 1;
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for (; k < a_n; k++) {
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assert(a[k] != (uint64_t)-1);
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assert(mm == (a[k]>>32));
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e = ((uint32_t)a[k]) + 1; p++;
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for (; ks < k; ks++) {
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if(e - ((uint32_t)a[ks]) <= winlen) break;
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p--;
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}
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assert(p >= 0);
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if(p > 0 && p >= (int64_t)(winlen*match_rate)) return 1;
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}
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return 0;
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}
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uint32_t ul_homo_path_check(ul_resolve_t *uidx, ma_ug_t *ug, uint32_t v, uint32_t w, uint32_t raw_ug_occ, float match_rate, asg64_v *b, asg64_v *rb)
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{
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// if(((v>>1) == 8158 && (w>>1) == 22318) || ((v>>1) == 16783 && (w>>1) == 28464)) {
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// fprintf(stderr, "\n++++++[M::%s::] v>>1::%u, v&1::%u, w>>1::%u, w&1::%u\n",
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// __func__, v>>1, v&1, w>>1, w&1);
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// }
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bubble_type *bub = uidx->bub;
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uint64_t k, l, z, bn = b->n, vn = 0, wn = 0, *va, *wa, rbn = rb->n, *rva, *rwa, rvn, rwn, rid, x;
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get_ul_path_info(uidx, ug, v, NULL, NULL, NULL, NULL, NULL, b); vn = b->n - bn;
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get_ul_path_info(uidx, ug, w, NULL, NULL, NULL, NULL, NULL, b); wn = b->n - bn - vn;
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va = b->a + bn; wa = b->a + bn + vn;
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// if(((v>>1) == 8158 && (w>>1) == 22318) || ((v>>1) == 16783 && (w>>1) == 28464)) {
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// fprintf(stderr, "[M::%s::] vn::%lu, wn::%lu\n", __func__, vn, wn);
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// }
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gen_ug_integer_seq_on_fly(uidx, va, vn, rb); rvn = rb->n - rbn;
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gen_ug_integer_seq_on_fly(uidx, wa, wn, rb); rwn = rb->n - rbn - rvn;
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rva = rb->a + rbn; rwa = rb->a + rbn + rvn;
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if(rvn > raw_ug_occ) rvn = raw_ug_occ;
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if(rwn > raw_ug_occ) rwn = raw_ug_occ;
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// if(((v>>1) == 8158 && (w>>1) == 22318) || ((v>>1) == 16783 && (w>>1) == 28464)) {
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// fprintf(stderr, "[M::%s::] rvn::%lu, rwn::%lu, raw_ug_occ::%u\n", __func__, rvn, rwn, raw_ug_occ);
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// }
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b->n = bn;
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for (k = 0; k < rvn; k++) {
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rid = rva[k]>>1;
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if(IF_BUB(rid, *bub)) {
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x = bub->index[rid]; x |= ((uint64_t)(0x80000000)); x <<= 32;
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x = bub->index[rid];
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x |= ((uint64_t)(0x80000000)); x <<= 32; ///bubble id
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} else {
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x = rid; x <<= 32;
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x = rid; ///node id
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x <<= 32;
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}
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kv_push(uint64_t, *b, x);
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x |= (k<<1); kv_push(uint64_t, *b, x);
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}
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for (k = 0; k < rwn; k++) {
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rid = rwa[k]>>1;
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if(IF_BUB(rid, *bub)) {
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x = bub->index[rid]; x |= ((uint64_t)(0x80000000)); x <<= 32;
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x = bub->index[rid];
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x |= ((uint64_t)(0x80000000)); x <<= 32; ///bubble id
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} else {
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x = rid; x <<= 32;
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x = rid; ///node id
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x <<= 32;
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}
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x |= 1; kv_push(uint64_t, *b, x);
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x |= 1; x |= (k<<1); kv_push(uint64_t, *b, x);
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}
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radix_sort_srt64(b->a + bn, b->a + b->n);
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uint64_t o[2];
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uint64_t o[2], c[2];
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for (l = bn, k = bn + 1, o[0] = o[1] = 0; k <= b->n; k++) {
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if (k == b->n || (b->a[k]>>32) != (b->a[l]>>32)) {
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if((k - l > 1) && (((uint32_t)b->a[l]) != ((uint32_t)b->a[k-1]))) {
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for (z = l; z < k; z++) o[(uint32_t)b->a[z]]++;
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if((k - l > 1)) {
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for (z = l, c[0] = c[1] = 0; z < k; z++) {
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c[b->a[z]&1]++;
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if(c[0] > 0 && c[1] > 0) break;
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}
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if(c[0] > 0 && c[1] > 0) {
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for (z = l; z < k; z++) {
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o[b->a[z]&1]++;
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x = b->a[z];
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x <<= 32; x >>= 32; x >>= 1;
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if(b->a[z]&1) x|= ((uint64_t)(0x100000000));
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b->a[z] = x;
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}
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} else {
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for (z = l; z < k; z++) b->a[z] = (uint64_t)-1;
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}
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} else {
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for (z = l; z < k; z++) b->a[z] = (uint64_t)-1;
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}
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l = k;
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}
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}
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// fprintf(stderr, "\n[M::%s::] rvn::%lu, rwn::%lu, bn::%lu, b->n::%lu, o[0]::%lu, o[1]::%lu\n", __func__,
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// rvn, rwn, bn, (uint64_t)b->n, o[0], o[1]);
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radix_sort_srt64(b->a + bn, b->a + b->n); b->n = bn + o[0] + o[1];
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b->n = bn; rb->n = rbn;
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if(o[0] >= (rvn*match_rate)) return 1;
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if(o[1] >= (rwn*match_rate)) return 1;
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if(idx_check_rate(b->a + bn, o[0], rvn, raw_ug_occ, match_rate)) return 1;
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if(idx_check_rate(b->a + bn + o[0], o[1], rwn, raw_ug_occ, match_rate)) return 1;
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// if(o[0] >= (rvn*match_rate)) return 1;
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// if(o[1] >= (rwn*match_rate)) return 1;
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return 0;
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}
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@@ -8413,6 +8482,10 @@ uint32_t skip_hom, uint32_t *max_drop_len, asg64_v *in, asg64_v *ib)
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for (i = 0; i < nv; ++i) {
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if(av[i].del) continue;
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kw = get_arcs(ug->g, av[i].v^1, NULL, 0);
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// if((v>>1) == 16783) {
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// fprintf(stderr, "sss[M::%s::] v>>1::%u, v&1::%u, av[i].v>>1::%u, av[i].v&1::%u, kw::%u\n",
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// __func__, v>>1, v&1, av[i].v>>1, av[i].v&1, kw);
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// }
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if(kw == 2) {
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kv_push(uint64_t, *b, ((uint64_t)(av-g->arc+i)));
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} else if(kw == 1) {
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@@ -8453,6 +8526,10 @@ uint32_t skip_hom, uint32_t *max_drop_len, asg64_v *in, asg64_v *ib)
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}
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if(kv <= 1 && kw <= 1) continue;
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if(kv != 2 || kw > 2) continue;
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, w>>1::%u, w&1::%u, kv::%u, kw::%u\n",
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// __func__, v>>1, v&1, w>>1, w&1, kv, kw);
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// }
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raw_ul = 0; wt = w; wte = we; kwt = kw; pb = b->n; ub->n = 0;
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if(kw == 1) {
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if(get_ul_path_info(uidx, ug, w^1, &wt, NULL, NULL, NULL, NULL, b)==TWO_INPUT) {
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@@ -8468,16 +8545,27 @@ uint32_t skip_hom, uint32_t *max_drop_len, asg64_v *in, asg64_v *ib)
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else wp[1] = aw[i].v;
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kwt++;
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}
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, w>>1::%u, w&1::%u, wt>>1::%u, wt&1::%u, kwt::%u\n",
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// __func__, v>>1, v&1, w>>1, w&1, wt>>1, wt&1, kwt);
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// }
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nw = asg_arc_n(g, w); aw = asg_arc_a(g, w);
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} else {
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b->n = pb;
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continue;
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}
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}
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, raw_ul::%lu, max_ext::%u, ***1***\n",
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// __func__, v>>1, v&1, raw_ul, max_ext);
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// }
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assert(kv == 2 && kwt == 2);
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if(raw_ul <= max_ext && get_remove_hifi_occ(uidx, max_ext_hifi, b->a + pb, b->n - pb, ub, NULL)) {
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raw_hifi = get_ug_integer_seq_occ(uidx, b->a + pb, b->n - pb, ub);
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, ***2***\n",
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// __func__, v>>1, v&1);
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// }
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b->n = pb;
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if(raw_ul > 0) {
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@@ -8487,20 +8575,44 @@ uint32_t skip_hom, uint32_t *max_drop_len, asg64_v *in, asg64_v *ib)
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if(!ul_occ_check(uidx, ug, raw_ul, raw_hifi, wp[1], small_occ_rate, b, ub)) continue;
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}
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, ***3***\n",
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// __func__, v>>1, v&1);
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// }
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pb = b->n; ub->n = 0;
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get_ul_arc_supports(uidx, ve, b, ub, skip_hom, &w_q, &w_t);
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b->n = pb; ub->n = 0;
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if((w_q == (uint64_t)-1) || (w_q > w_t*len_rat)) continue;
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, ***4***\n",
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// __func__, v>>1, v&1);
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// }
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pb = b->n; ub->n = 0;
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get_ul_arc_supports(uidx, wte, b, ub, skip_hom, &w_q, &w_t);
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b->n = pb; ub->n = 0;
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if((w_q == (uint64_t)-1) || (w_q > w_t*len_rat)) continue;
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, ***5***\n",
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// __func__, v>>1, v&1);
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// }
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if(!ul_homo_path_check(uidx, ug, vp[0], wp[1], raw_ug_occ, raw_match_rate, b, ub)) continue;
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, ***6***\n",
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// __func__, v>>1, v&1);
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// }
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if(!ul_homo_path_check(uidx, ug, wp[0], vp[1], raw_ug_occ, raw_match_rate, b, ub)) continue;
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// if((v>>1) == 16783) {
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// fprintf(stderr, "bbb[M::%s::] v>>1::%u, v&1::%u, ***7***\n",
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// __func__, v>>1, v&1);
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// }
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if(kw == 1) {
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get_ul_path_info(uidx, ug, w^1, &wt, NULL, NULL, NULL, NULL, b);
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for (z = pb; z < b->n; z++) ulg_seq_del(ug, (b->a[z]>>1));
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@@ -8515,51 +8627,54 @@ uint32_t skip_hom, uint32_t *max_drop_len, asg64_v *in, asg64_v *ib)
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if(!in) free(tx.a); if(!ib) free(tb.a);
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if (cnt > 0) asg_cleanup(g);
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fprintf(stderr, "[M::%s::] cnt::%u\n", __func__, cnt);
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return cnt;
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}
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void u2g_clean(ul_resolve_t *uidx, ulg_opt_t *ulopt)
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{
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ul2ul_idx_t *idx = &(uidx->uovl); asg64_v bu = {0,0,0}, uu = {0,0,0};
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ma_ug_t *iug = idx->i_ug; int64_t i, mm_tip = ulopt->max_tip; uint64_t cnt = 1, topo_level;
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ma_ug_t *iug = idx->i_ug; int64_t i, mm_tip = ulopt->max_tip; uint64_t cnt = 1, topo_level, ss = 0;
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double step = (ulopt->clean_round==1?ulopt->max_ovlp_drop_ratio:
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((ulopt->max_ovlp_drop_ratio-ulopt->min_ovlp_drop_ratio)/(ulopt->clean_round-1)));
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double drop = ulopt->min_ovlp_drop_ratio; CALLOC(iug->g->seq_vis, iug->g->n_seq*2);
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// ulg_arc_cut_tips(uidx, iug, ulopt->max_tip, ulopt->max_tip_hifi, &bu, &uu);
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for (i = 0, drop = ulopt->min_ovlp_drop_ratio; i < ulopt->clean_round; i++, drop += step) {
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fprintf(stderr, "\n[M::%s::] Starting round-%ld, drop::%f\n", __func__, i, drop);
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cnt = 1; topo_level = 2; mm_tip = ulopt->max_tip;
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while (cnt) {
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cnt = 0;
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asg_arc_identify_simple_bubbles_multi(iug->g, ulopt->b_mask_t, 0);
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cnt += ulg_arc_cut_supports(uidx, iug, mm_tip, ulopt->max_tip_hifi, drop, ulopt->is_trio, topo_level, 1, NULL, &bu, &uu);
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cnt += ulg_arc_cut_tips(uidx, iug, mm_tip, ulopt->max_tip_hifi, &bu, &uu);
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}
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cnt = 1; topo_level = 1; mm_tip = ulopt->max_tip;
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while (cnt) {
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cnt = 0;
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asg_arc_identify_simple_bubbles_multi(iug->g, ulopt->b_mask_t, 0);
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cnt += ulg_arc_cut_supports(uidx, iug, mm_tip, ulopt->max_tip_hifi, drop, ulopt->is_trio, topo_level, 1, NULL, &bu, &uu);
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cnt += ulg_arc_cut_tips(uidx, iug, mm_tip, ulopt->max_tip_hifi, &bu, &uu);
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for (ss = 0; ss < 2; ss++) {
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for (i = 0, drop = ulopt->min_ovlp_drop_ratio; i < ulopt->clean_round; i++, drop += step) {
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fprintf(stderr, "\n[M::%s::] Starting round-%ld, drop::%f\n", __func__, i, drop);
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cnt = 1; topo_level = 2; mm_tip = ulopt->max_tip;
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while (cnt) {
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cnt = 0;
|
||||
asg_arc_identify_simple_bubbles_multi(iug->g, ulopt->b_mask_t, 0);
|
||||
cnt += ulg_arc_cut_supports(uidx, iug, mm_tip, ulopt->max_tip_hifi, drop, ulopt->is_trio, topo_level, 1, NULL, &bu, &uu);
|
||||
cnt += ulg_arc_cut_tips(uidx, iug, mm_tip, ulopt->max_tip_hifi, 1, &bu, &uu);
|
||||
}
|
||||
|
||||
cnt = 1; topo_level = 1; mm_tip = ulopt->max_tip;
|
||||
while (cnt) {
|
||||
cnt = 0;
|
||||
asg_arc_identify_simple_bubbles_multi(iug->g, ulopt->b_mask_t, 0);
|
||||
cnt += ulg_arc_cut_supports(uidx, iug, mm_tip, ulopt->max_tip_hifi, drop, ulopt->is_trio, topo_level, 1, NULL, &bu, &uu);
|
||||
cnt += ulg_arc_cut_tips(uidx, iug, mm_tip, ulopt->max_tip_hifi, 1, &bu, &uu);
|
||||
}
|
||||
|
||||
cnt = 1; topo_level = 1; mm_tip = ((int64_t)0x7fffffff);
|
||||
while (cnt) {
|
||||
cnt = 0;
|
||||
asg_arc_identify_simple_bubbles_multi(iug->g, ulopt->b_mask_t, 0);
|
||||
cnt += ulg_arc_cut_supports(uidx, iug, mm_tip, ulopt->max_tip_hifi, drop, ulopt->is_trio, topo_level, 1, NULL, &bu, &uu);
|
||||
cnt += ulg_arc_cut_tips(uidx, iug, mm_tip, ulopt->max_tip_hifi, 0, &bu, &uu);
|
||||
}
|
||||
fprintf(stderr, "[M::%s::] Done round-%ld, drop::%f\n", __func__, i, drop);
|
||||
}
|
||||
|
||||
cnt = 1; topo_level = 1; mm_tip = ((int64_t)0x7fffffff);
|
||||
while (cnt) {
|
||||
cnt = 0;
|
||||
asg_arc_identify_simple_bubbles_multi(iug->g, ulopt->b_mask_t, 0);
|
||||
cnt += ulg_arc_cut_supports(uidx, iug, mm_tip, ulopt->max_tip_hifi, drop, ulopt->is_trio, topo_level, 1, NULL, &bu, &uu);
|
||||
cnt += ulg_arc_cut_tips(uidx, iug, mm_tip, ulopt->max_tip_hifi, &bu, &uu);
|
||||
}
|
||||
fprintf(stderr, "[M::%s::] Done round-%ld, drop::%f\n", __func__, i, drop);
|
||||
ulg_pop_bubble(uidx, iug, NULL, ((int64_t)0x7fffffff), ulopt->max_tip_hifi, 1, &bu, &uu);
|
||||
|
||||
while(ulg_arc_cut_z(uidx, iug, ((int64_t)0x7fffffff), ulopt->max_tip_hifi, 1.5, 0.15, 100, 0.8, ulopt->is_trio, 1, NULL, &bu, &uu));
|
||||
|
||||
ulopt->max_tip_hifi <<= 1;
|
||||
}
|
||||
|
||||
ulg_pop_bubble(uidx, iug, NULL, ((int64_t)0x7fffffff), ulopt->max_tip_hifi, 1, &bu, &uu);
|
||||
|
||||
while(ulg_arc_cut_z(uidx, iug, ((int64_t)0x7fffffff), ulopt->max_tip_hifi, 1.5, 0.15, 100, 0.8, ulopt->is_trio, 1, NULL, &bu, &uu));
|
||||
|
||||
// fill_u2g(uidx);
|
||||
|
||||
// while (cnt) {
|
||||
@@ -9059,7 +9174,7 @@ ul2ul_idx_t *gen_ul2ul(ul_resolve_t *uidx, ug_opt_t *uopt, ulg_opt_t *ulopt)
|
||||
|
||||
// output_integer_graph(uidx, z->i_ug, asm_opt.output_file_name);
|
||||
u2g_clean(uidx, ulopt);
|
||||
// renew_ul2_utg(uidx);
|
||||
renew_ul2_utg(uidx);
|
||||
|
||||
output_integer_graph(uidx, z->i_ug, asm_opt.output_file_name);
|
||||
return z;
|
||||
|
||||
Reference in New Issue
Block a user