mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-26 05:38:11 +08:00
reomve redundancy
This commit is contained in:
chhylp123
+325
-140
@@ -8759,69 +8759,6 @@ static char comp_tab[] = { // complement base
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'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
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};
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// generate unitig sequences
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int ma_ug_seq_back(ma_ug_t *g, All_reads *RNF, const ma_sub_t *coverage_cut,
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const long long n_read)
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{
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UC_Read g_read;
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init_UC_Read(&g_read);
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utg_intv_t *tmp;
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uint32_t i, j;
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///why we need n_read here? it is just beacuse one read can only be included in one untig
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///but it is not true
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tmp = (utg_intv_t*)calloc(n_read, sizeof(utg_intv_t));
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///number of unitigs
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for (i = 0; i < g->u.n; ++i) {
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ma_utg_t *u = &g->u.a[i];
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uint32_t l = 0;
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u->s = (char*)calloc(1, u->len + 1);
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memset(u->s, 'N', u->len);
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for (j = 0; j < u->n; ++j) {
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///u->a[j]>>33 is the readID
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utg_intv_t *t = &tmp[u->a[j]>>33];
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///assert(t->len == 0);
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t->utg = i, t->ori = u->a[j]>>32&1;
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///l is the start pos of this read at its corresponding untig
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t->start = l, t->len = (uint32_t)u->a[j];
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l += t->len;
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}
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}
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int32_t id;
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for (id = 0; id < n_read; id++)
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{
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utg_intv_t *t;
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ma_utg_t *u;
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if (id < 0 || tmp[id].len == 0) continue;
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t = &tmp[id];
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u = &g->u.a[t->utg];
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recover_UC_Read(&g_read, RNF, id);
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memmove(g_read.seq, g_read.seq + coverage_cut[id].s, coverage_cut[id].e - coverage_cut[id].s);
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g_read.length = coverage_cut[id].e - coverage_cut[id].s;
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if (!t->ori) { // forward strand
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for (i = 0; i < t->len; ++i)
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u->s[t->start + i] = g_read.seq[i];
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} else {
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for (i = 0; i < t->len; ++i) {
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int c = (uint8_t)g_read.seq[g_read.length - 1 - i];
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u->s[t->start + i] = c >= 128? 'N' : comp_tab[c];
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}
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}
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}
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free(tmp);
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destory_UC_Read(&g_read);
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return 0;
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}
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void recover_fake_read(UC_Read* result, UC_Read* tmp, ma_utg_t *u,
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All_reads *RNF, const ma_sub_t *coverage_cut)
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@@ -9127,6 +9064,14 @@ ma_sub_t *coverage_cut, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
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if(pre == (uint32_t)-1) continue;
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if(afte == (uint32_t)-1) continue;
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/****************************may have bugs********************************/
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///if(debug_purge_dup == 1 && ((v>>1)==1239235 || (v>>1)==4576917 || (v>>1)==4479766))
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if(debug_purge_dup == 1 && (v>>1)==4576917)
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{
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fprintf(stderr, "v>>1: %u, pre>>1: %u, afte>>1: %u, len: %u\n", v>>1, pre>>1, afte>>1, collection->len);
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}
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/****************************may have bugs********************************/
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av = asg_arc_a(read_g, v^1);
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nv = asg_arc_n(read_g, v^1);
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for (k = 0; k < nv; k++)
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@@ -9177,8 +9122,15 @@ ma_sub_t *coverage_cut, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
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}
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}
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if(k == edge->a.n) fprintf(stderr, "ERROR\n");
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}
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}
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/****************************may have bugs********************************/
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///if(debug_purge_dup == 1 && ((v>>1)==1239235 || (v>>1)==4576917 || (v>>1)==4479766))
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if(debug_purge_dup == 1 && (v>>1)==4576917)
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{
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fprintf(stderr, "v>>1: %u, pE->el: %u, aE->el: %u\n", v>>1, pE->el, aE->el);
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}
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/****************************may have bugs********************************/
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if(pE->el == 1 && aE->el == 1) continue;
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@@ -9195,6 +9147,304 @@ ma_sub_t *coverage_cut, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
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continue;
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}
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/****************************may have bugs********************************/
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///if(debug_purge_dup == 1 && ((v>>1)==1239235 || (v>>1)==4576917 || (v>>1)==4479766))
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if(debug_purge_dup == 1 && (v>>1)==4576917)
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{
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fprintf(stderr, "v>>1: %u, t_f.el: %u, t_b.el: %u\n", v>>1, t_f.el, t_b.el);
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}
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/****************************may have bugs********************************/
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if(t_f.el == 0 || t_b.el == 0) continue;
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get_overlapLen(v>>1, sources, &exactLen, &inexactLen);
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if(pE->el == 0)
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{
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get_overlapLen(pre>>1, sources, &tmp_exactLen, &tmp_inexactLen);
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/****************************may have bugs********************************/
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///if(debug_purge_dup == 1 && ((v>>1)==1239235 || (v>>1)==4576917 || (v>>1)==4479766))
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if(debug_purge_dup == 1 && (v>>1)==4576917)
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{
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fprintf(stderr, "v>>1: %u, exactLen: %u, inexactLen: %u, tmp_exactLen: %u, tmp_inexactLen: %u\n",
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v>>1, exactLen, inexactLen, tmp_exactLen, tmp_inexactLen);
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}
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/****************************may have bugs********************************/
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if(inexactLen < tmp_inexactLen) continue;
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if(inexactLen == tmp_inexactLen && exactLen > tmp_exactLen) continue;
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}
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if(aE->el == 0)
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{
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get_overlapLen(afte>>1, sources, &tmp_exactLen, &tmp_inexactLen);
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if(inexactLen < tmp_inexactLen) continue;
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if(inexactLen == tmp_inexactLen && exactLen > tmp_exactLen) continue;
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}
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/****************************may have bugs********************************/
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///if(debug_purge_dup == 1 && ((v>>1)==1239235 || (v>>1)==4576917 || (v>>1)==4479766))
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if(debug_purge_dup == 1 && (v>>1)==4576917)
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{
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fprintf(stderr, "v>>1: %u, i: %u\n", v>>1, i);
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}
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/****************************may have bugs********************************/
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collection->a[i] = (uint64_t)-1;
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skip++;
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}
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if(skip == 0) return 0;
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m = 0;
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for (i = 0; i < collection->n; i++)
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{
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if(collection->a[i] == (uint64_t)-1) continue;
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collection->a[m] = collection->a[i];
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m++;
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}
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collection->n = m;
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uint32_t totalLen = 0, w, l;
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for (i = 0; i < collection->n - 1; i++)
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{
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v = (uint64_t)(collection->a[i])>>32;
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w = (uint64_t)(collection->a[i + 1])>>32;
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/*******************************for debug************************************/
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l = (uint32_t)-1;
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av = asg_arc_a(read_g, v);
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nv = asg_arc_n(read_g, v);
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for (k = 0; k < nv; k++)
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{
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if(av[k].del) continue;
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if(av[k].v == w)
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{
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l = asg_arc_len(av[k]);
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break;
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}
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}
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if(k == nv)
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{
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for (k = 0; k < edge->a.n; k++)
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{
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if(edge->a.a[k].del) continue;
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if((edge->a.a[k].ul>>32) == v && edge->a.a[k].v == w)
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{
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l = asg_arc_len(edge->a.a[k]);
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break;
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}
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}
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if(k == edge->a.n)
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{
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if(get_edge_from_source(sources, coverage_cut, NULL, max_hang, min_ovlp, v, w, &t_f)==0)
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{
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fprintf(stderr, "####ERROR1: v>>1: %u, v&1: %u, w>>1: %u, w&1: %u, r_seq: %u\n",
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v>>1, v&1, w>>1, w&1, read_g->r_seq);
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}
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l = asg_arc_len(t_f);
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}
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}
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if(l == (uint32_t)-1) fprintf(stderr, "ERROR\n");
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/*******************************for debug************************************/
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collection->a[i] = v; collection->a[i] = collection->a[i]<<32;
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collection->a[i] = collection->a[i] | (uint64_t)(l);
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totalLen += l;
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}
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if(i < collection->n)
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{
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if(collection->circ)
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{
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v = (uint64_t)(collection->a[i])>>32;
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w = (uint64_t)(collection->a[0])>>32;
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/*******************************for debug************************************/
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l = (uint32_t)-1;
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av = asg_arc_a(read_g, v);
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nv = asg_arc_n(read_g, v);
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for (k = 0; k < nv; k++)
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{
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if(av[k].del) continue;
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if(av[k].v == w)
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{
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l = asg_arc_len(av[k]);
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break;
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}
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}
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if(k == nv)
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{
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for (k = 0; k < edge->a.n; k++)
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{
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if(edge->a.a[k].del) continue;
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if((edge->a.a[k].ul>>32) == v && edge->a.a[k].v == w)
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{
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l = asg_arc_len(edge->a.a[k]);
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break;
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}
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}
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if(k == edge->a.n)
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{
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if(get_edge_from_source(sources, coverage_cut, NULL, max_hang, min_ovlp, v, w, &t_f)==0)
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{
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fprintf(stderr, "####ERROR1: v>>1: %u, v&1: %u, w>>1: %u, w&1: %u, r_seq: %u\n",
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v>>1, v&1, w>>1, w&1, read_g->r_seq);
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}
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l = asg_arc_len(t_f);
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}
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}
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if(l == (uint32_t)-1) fprintf(stderr, "ERROR\n");
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/*******************************for debug************************************/
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collection->a[i] = v; collection->a[i] = collection->a[i]<<32;
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collection->a[i] = collection->a[i] | (uint64_t)(l);
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totalLen += l;
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}
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else
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{
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v = (uint64_t)(collection->a[i])>>32;
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l = read_g->seq[v>>1].len;
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collection->a[i] = v;
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collection->a[i] = collection->a[i]<<32;
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collection->a[i] = collection->a[i] | (uint64_t)(l);
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totalLen += l;
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}
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}
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collection->len = totalLen;
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if(!collection->circ)
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{
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collection->start = collection->a[0]>>32;
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collection->end = (collection->a[collection->n-1]>>32)^1;
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}
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return 1;
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}
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uint32_t polish_unitig_advance(ma_utg_t* collection, asg_t* read_g, ma_hit_t_alloc* sources,
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ma_sub_t *coverage_cut, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
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{
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if(collection->m == 0) return 0;
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if(collection->n < 2) return 0;
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uint32_t i, k, v, pre, afte, nv, exactLen, inexactLen, tmp_exactLen, tmp_inexactLen, m = 0, skip = 0;
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asg_arc_t* av = NULL;
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asg_arc_t *pE = NULL, *aE = NULL;
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asg_arc_t t_f, t_b;
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for (i = 1; i < collection->n; i++)
|
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{
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v = (uint64_t)(collection->a[i])>>32;
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pre = (uint64_t)(collection->a[i-1])>>32;
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afte = (uint64_t)(collection->a[i+1])>>32;
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if(v == (uint32_t)-1) continue;
|
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if(pre == (uint32_t)-1) continue;
|
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if(afte == (uint32_t)-1) continue;
|
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|
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av = asg_arc_a(read_g, v^1);
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nv = asg_arc_n(read_g, v^1);
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for (k = 0; k < nv; k++)
|
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{
|
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if(av[k].del) continue;
|
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if(av[k].v == (pre^1))
|
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{
|
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pE = &(av[k]);
|
||||
break;
|
||||
}
|
||||
}
|
||||
if(k == nv)
|
||||
{
|
||||
for (k = 0; k < edge->a.n; k++)
|
||||
{
|
||||
if(edge->a.a[k].del) continue;
|
||||
if((edge->a.a[k].ul>>32) == (v^1) && edge->a.a[k].v == (pre^1))
|
||||
{
|
||||
pE = &(edge->a.a[k]);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if(k == edge->a.n) fprintf(stderr, "ERROR\n");
|
||||
}
|
||||
|
||||
av = asg_arc_a(read_g, v);
|
||||
nv = asg_arc_n(read_g, v);
|
||||
for (k = 0; k < nv; k++)
|
||||
{
|
||||
if(av[k].del) continue;
|
||||
if(av[k].v == afte)
|
||||
{
|
||||
aE = &(av[k]);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if(k == nv)
|
||||
{
|
||||
for (k = 0; k < edge->a.n; k++)
|
||||
{
|
||||
if(edge->a.a[k].del) continue;
|
||||
if((edge->a.a[k].ul>>32) == v && edge->a.a[k].v == afte)
|
||||
{
|
||||
aE = &(edge->a.a[k]);
|
||||
break;
|
||||
}
|
||||
}
|
||||
if(k == edge->a.n) fprintf(stderr, "ERROR\n");
|
||||
}
|
||||
|
||||
|
||||
if(pE->el == 1 && aE->el == 1) continue;
|
||||
|
||||
if(get_edge_from_source(sources, coverage_cut, NULL, max_hang, min_ovlp, pre,
|
||||
afte, &t_f) == 0)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
|
||||
if(get_edge_from_source(sources, coverage_cut, NULL, max_hang, min_ovlp, afte^1,
|
||||
pre^1, &t_b) == 0)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
|
||||
|
||||
if(t_f.el == 0 || t_b.el == 0) continue;
|
||||
|
||||
get_overlapLen(v>>1, sources, &exactLen, &inexactLen);
|
||||
@@ -9212,6 +9462,7 @@ ma_sub_t *coverage_cut, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
|
||||
if(inexactLen == tmp_inexactLen && exactLen > tmp_exactLen) continue;
|
||||
}
|
||||
|
||||
|
||||
collection->a[i] = (uint64_t)-1;
|
||||
skip++;
|
||||
}
|
||||
@@ -9375,76 +9626,6 @@ ma_sub_t *coverage_cut, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
|
||||
return 1;
|
||||
}
|
||||
// generate unitig sequences
|
||||
int ma_ug_seq_back(ma_ug_t *g, asg_t *read_g, All_reads *RNF, const ma_sub_t *coverage_cut)
|
||||
{
|
||||
UC_Read g_read;
|
||||
init_UC_Read(&g_read);
|
||||
UC_Read tmp;
|
||||
init_UC_Read(&tmp);
|
||||
///utg_intv_t *tmp;
|
||||
uint32_t i, j, k;
|
||||
uint32_t rId, /**uId,**/ori, start, eLen, readLen;
|
||||
char* readS = NULL;
|
||||
|
||||
|
||||
///why we need n_read here? it is just beacuse one read can only be included in one untig
|
||||
///but it is not true
|
||||
///tmp = (utg_intv_t*)calloc(n_read, sizeof(utg_intv_t));
|
||||
///number of unitigs
|
||||
for (i = 0; i < g->u.n; ++i) {
|
||||
ma_utg_t *u = &g->u.a[i];
|
||||
if(u->m == 0) continue;
|
||||
|
||||
uint32_t l = 0;
|
||||
u->s = (char*)calloc(1, u->len + 1);
|
||||
memset(u->s, 'N', u->len);
|
||||
for (j = 0; j < u->n; ++j) {
|
||||
rId = u->a[j]>>33;
|
||||
///uId = i;
|
||||
ori = u->a[j]>>32&1;
|
||||
start = l;
|
||||
eLen = (uint32_t)u->a[j];
|
||||
l += eLen;
|
||||
|
||||
if(eLen == 0) continue;
|
||||
if(rId < read_g->r_seq)
|
||||
{
|
||||
recover_UC_Read(&g_read, RNF, rId);
|
||||
}
|
||||
else
|
||||
{
|
||||
recover_fake_read(&g_read, &tmp, &(read_g->F_seq[rId-read_g->r_seq]),
|
||||
RNF, coverage_cut);
|
||||
}
|
||||
|
||||
readS = g_read.seq + coverage_cut[rId].s;
|
||||
readLen = coverage_cut[rId].e - coverage_cut[rId].s;
|
||||
|
||||
if (!ori) // forward strand
|
||||
{
|
||||
for (k = 0; k < eLen; k++)
|
||||
{
|
||||
u->s[start + k] = readS[k];
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
for (k = 0; k < eLen; k++)
|
||||
{
|
||||
uint8_t c = (uint8_t)readS[readLen - 1 - k];
|
||||
u->s[start + k] = c >= 128? 'N' : comp_tab[c];
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
destory_UC_Read(&g_read);
|
||||
destory_UC_Read(&tmp);
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -9553,8 +9734,8 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
|
||||
if(tn == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[tn].del == 1) continue;
|
||||
}
|
||||
if(read_g->seq[tn].del == 1) continue;
|
||||
if(r_flag[tn] != 1) continue;
|
||||
C_bases += (Get_qe((*h)) - Get_qs((*h)));
|
||||
if(r_flag[tn] != 1) continue;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -23015,8 +23196,13 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
|
||||
adjust_utg_by_primary(&ug, sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
|
||||
bubble_dist, tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
|
||||
max_hang, min_ovlp, &new_rtg_edges);
|
||||
|
||||
/****************************may have bugs********************************/
|
||||
debug_purge_dup = 1;
|
||||
/****************************may have bugs********************************/
|
||||
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp);
|
||||
/****************************may have bugs********************************/
|
||||
debug_purge_dup = 0;
|
||||
/****************************may have bugs********************************/
|
||||
|
||||
|
||||
fprintf(stderr, "Writing primary contig GFA to disk... \n");
|
||||
@@ -27168,10 +27354,9 @@ long long bubble_dist, int read_graph, int write)
|
||||
&R_INF, output_file_name);
|
||||
}
|
||||
|
||||
debug_info_of_specfic_read("m64062_190803_042216/120916077/ccs", sources, reverse_sources, -1, "beg");
|
||||
debug_info_of_specfic_read("m64062_190806_063919/71436446/ccs", sources, reverse_sources, -1, "beg");
|
||||
debug_info_of_specfic_read("m64062_190803_042216/82117654/ccs", sources, reverse_sources, -1, "beg");
|
||||
|
||||
debug_info_of_specfic_read("m64062_190803_042216/177341795/ccs", sources, reverse_sources, -1, "beg");
|
||||
// debug_info_of_specfic_read("m64062_190807_194840/126682874/ccs", sources, reverse_sources, -1, "beg");
|
||||
exit(1);
|
||||
|
||||
if (!(asm_opt.flag & HA_F_BAN_ASSEMBLY))
|
||||
{
|
||||
|
||||
Reference in New Issue
Block a user