mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-30 22:18:12 +08:00
fix bugs for overlaps of different length
This commit is contained in:
Haoyu Cheng
+554
-30
@@ -884,6 +884,106 @@ long long mini_overlap_length, ma_sub_t** coverage_cut)
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void ma_hit_chimeric(int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
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long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut)
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{
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double startTime = Get_T();
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int i, j, k, n_remove = 0;
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kvec_t(uint32_t) b = {0,0,0};
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for (i = 0; i < n_read; ++i)
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{
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kv_resize(uint32_t, b, readLen[i]);
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memset(b.a, 0, sizeof(uint32_t)*readLen[i]);
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for (j = 0; j < sources[i].length; j++)
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{
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uint32_t qs, qe;
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qs = Get_qs(sources[i].buffer[j]);
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qe = Get_qe(sources[i].buffer[j]);
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///if(qe - qs < 1000) continue;
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for (k = qs; k < qe; k++)
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{
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b.a[k]++;
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}
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}
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// for (j = 0; j < reverse_sources[i].length; j++)
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// {
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// uint32_t qs, qe;
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// qs = Get_qs(reverse_sources[i].buffer[j]);
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// qe = Get_qe(reverse_sources[i].buffer[j]);
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// for (k = qs; k < qe; k++)
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// {
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// b.a[k]++;
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// }
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// }
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int left, right;
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left = -1;
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right = readLen[i];
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for (k = 0; k < readLen[i]; k++)
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{
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if(b.a[k] < min_dp)
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{
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left = k;
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break;
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}
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}
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for (k = readLen[i] - 1; k >= 0; k--)
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{
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if(b.a[k] < min_dp)
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{
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right = k;
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break;
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}
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}
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// if(i == 4616942 || i == 4024299 || i == 6135193)
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// {
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// fprintf(stderr, "i: %d, left: %d, right: %d, rLen: %d, min_dp: %d\n",
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// i, left, right, readLen[i], min_dp);
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// for (k = 0; k < readLen[i]; k++)
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// {
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// fprintf(stderr, "a[%d]: %d\n", k, b.a[k]);
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// }
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// }
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if( (left <= right) && (left > 0) && (right < readLen[i] - 1))
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{
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coverage_cut[i].c = 1;
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n_remove++;
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/****************************may have bugs********************************/
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coverage_cut[i].del = 1;
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sources[i].length = 0;
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/****************************may have bugs********************************/
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}
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else
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{
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coverage_cut[i].c = 0;
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}
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}
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free(b.a);
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fprintf(stderr, "[M::%s] takes %0.2f s, n_remove: %d\n\n", __func__, Get_T()-startTime, n_remove);
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}
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void ma_hit_cut(int min_dp, ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
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long long mini_overlap_length, ma_sub_t** coverage_cut)
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{
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@@ -1488,6 +1588,7 @@ int max_hang, int min_ovlp)
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{
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///if a read has been deleted, should we still add them?
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asg_seq_set(g, i, coverage_cut[i].e - coverage_cut[i].s, coverage_cut[i].del);
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g->seq[i].c = coverage_cut[i].c;
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}
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g->seq_vis = (uint8_t*)calloc(g->n_seq*2, sizeof(uint8_t));
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@@ -3889,15 +3990,6 @@ void* asg_arc_identify_simple_bubbles_pthread(void* arg)
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b.b.n = 0;
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///if(v%10000 == 0)
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//if(v >= 18020000)
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// if(v == 18021291)
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// {
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// fprintf(stderr, "0 v: %d, thr_ID: %d\n", v, thr_ID);
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// fflush(stderr);
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// }
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if(g->seq_vis[v] != 1)
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{
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///if(detect_bubble_with_bubbles(g, v, &w, &l, &b, (uint32_t)-1))
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@@ -6294,7 +6386,6 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
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/****************************may have bugs********************************/
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/**
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if(to_del_l != kv)
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{
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b_f.n = 0;
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@@ -6384,7 +6475,317 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
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}
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terminal:
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**/
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/****************************may have bugs********************************/
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if(to_del_l != kv) continue;
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uint32_t convex1;
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long long l1;
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////forward bubble
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to_del_l = 0;
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for (i = 0; i < b_f.n; i++)
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{
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if(b_f.a[i] == b_f.a[0])
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{
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to_del_l = 1;
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}
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else
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{
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to_del_l = 0;
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break;
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}
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}
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//check the length
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if(to_del_l == 0 && asg_bub_end_finder_with_del_advance(g,
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b_f.a, b_f.n, max_dist, &bub, 0, (u_int32_t)-1, &sink)==1)
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{
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to_del_l = 1;
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}
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if(to_del_l == 0 && detect_mul_bubble_end_with_bubbles(g, b_f.a, b_f.n, &convex1, &l1, NULL))
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{
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to_del_l = 1;
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}
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///if(v>>1 == 4581428) fprintf(stderr, "to_del_l: %d, b_f.n: %d\n", to_del_l, b_f.n);
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///if(to_del_l == 0) continue;
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////backward bubble
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to_del_r = 0;
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for (i = 0; i < b_r.n; i++)
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{
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if(b_r.a[i] == b_r.a[0])
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{
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to_del_r = 1;
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}
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else
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{
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to_del_r = 0;
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break;
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}
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}
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if(to_del_r == 0 && asg_bub_end_finder_with_del_advance
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(g, b_r.a, b_r.n, max_dist, &bub, 1, v^1, &sink)==1)
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{
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to_del_r = 1;
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}
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if(to_del_r == 0 && detect_mul_bubble_end_with_bubbles(g, b_r.a, b_r.n, &convex1, &l1, NULL))
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{
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to_del_r = 1;
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}
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// if(v>>1 == 4581428)
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// {
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// fprintf(stderr, "to_del_l: %d, b_f.n: %d\n", to_del_l, b_f.n);
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// asg_bub_end_finder_with_del_advance_debug(g, b_r.a, b_r.n, max_dist, &bub, 1, v^1);
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// }
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// if(v>>1 == 7318036)
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// {
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// fprintf(stderr, "to_del_l: %d, to_del_r: %d, b_f.n: %d\n", to_del_l, to_del_r, b_f.n);
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// }
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if (to_del_l && to_del_r)
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{
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for (i = 0; i < nv; ++i)
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{
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if (av[i].del) continue;
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///fprintf(stderr, "%.*s\n", Get_NAME_LENGTH((R_INF), v>>1), Get_NAME((R_INF), v>>1));
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++n_cut;
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av[i].del = 1;
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asg_arc_del(g, av[i].v^1, av[i].ul>>32^1, 1);
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}
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}
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}
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free(b.a); free(b_f.a); free(b_r.a);
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free(bub.a); free(bub.S.a); free(bub.T.a); free(bub.b.a); free(bub.e.a);
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if (n_cut)
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{
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asg_cleanup(g);
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asg_symm(g);
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}
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fprintf(stderr, "[M::%s] removed %d false overlaps\n", __func__, n_cut);
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fprintf(stderr, "[M::%s] takes %0.2f s\n\n", __func__, Get_T()-startTime);
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return n_cut;
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}
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int asg_arc_del_short_false_link_advance(asg_t *g, float drop_ratio, float o_drop_ratio, int max_dist,
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ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
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{
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double startTime = Get_T();
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kvec_t(uint64_t) b;
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memset(&b, 0, sizeof(b));
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kvec_t(uint32_t) b_f;
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memset(&b_f, 0, sizeof(b_f));
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kvec_t(uint32_t) b_r;
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memset(&b_r, 0, sizeof(b_r));
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uint32_t v, w, n_vtx = g->n_seq * 2, n_cut = 0;
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uint32_t sink;
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buf_t bub;
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if (!g->is_symm) asg_symm(g);
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memset(&bub, 0, sizeof(buf_t));
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bub.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
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for (v = 0; v < n_vtx; ++v)
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{
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if(g->seq_vis[v] == 0)
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{
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asg_arc_t *av = asg_arc_a(g, v);
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uint32_t nv = asg_arc_n(g, v);
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if(nv == 1 && asg_arc_n(g, v^1) == 1) continue;
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uint64_t t_ol = 0;
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long long i;
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for (i = 0; i < nv; ++i)
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{
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t_ol += av[i].ol;
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}
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kv_push(uint64_t, b, (uint64_t)(t_ol << 32 | v));
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}
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}
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fprintf(stderr, "[M::%s] %lld unsorted pending overlaps\n", __func__, b.n);
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radix_sort_arch64(b.a, b.a + b.n);
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fprintf(stderr, "[M::%s] %lld sorted pending overlaps\n", __func__, b.n);
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uint32_t min_edge;
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long long k, t;
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for (k = 0; k < b.n; k++)
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{
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///v is the node
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v = (uint32_t)b.a[k];
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if (g->seq[v>>1].del) continue;
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uint32_t nv = asg_arc_n(g, v), nw, to_del_l, to_del_r;
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if (nv < 2) continue;
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uint32_t kv = get_real_length(g, v, NULL), kw;
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if (kv < 2) continue;
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uint32_t i;
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asg_arc_t *av = asg_arc_a(g, v), *aw;
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b_f.n = 0;
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b_r.n = 0;
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to_del_l = 0;
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for (i = 0; i < nv; i++)
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{
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if (av[i].del) continue;
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w = av[i].v^1;
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nw = asg_arc_n(g, w);
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if(nw < 2) break;
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kw = get_real_length(g, w, NULL);
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if(kw < 2) break;
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kv_push(uint32_t, b_f, av[i].v);
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kv_push(uint32_t, b_r, w);
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aw = asg_arc_a(g, w);
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min_edge = (u_int32_t)-1;
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for (t = 0; t < nw; t++)
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{
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if(aw[t].del) continue;
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if((aw[t].v>>1) == (v>>1)) continue;
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if(aw[t].ol < min_edge) min_edge = aw[t].ol;
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///kv_push(uint32_t, b_r, aw[t].v);
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}
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if(av[i].ol < min_edge * drop_ratio) to_del_l++;
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}
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/****************************may have bugs********************************/
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if(to_del_l != kv)
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{
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b_f.n = 0;
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b_r.n = 0;
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to_del_l = 0;
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for (i = 0; i < nv; i++)
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{
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if (av[i].del) continue;
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w = av[i].v^1;
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nw = asg_arc_n(g, w);
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if(nw < 2) break;
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kw = get_real_length(g, w, NULL);
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if(kw < 2) break;
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kv_push(uint32_t, b_f, av[i].v);
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kv_push(uint32_t, b_r, w);
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aw = asg_arc_a(g, w);
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min_edge = (u_int32_t)-1;
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for (t = 0; t < nw; t++)
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{
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if(aw[t].del) continue;
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if((aw[t].v>>1) == (v>>1)) continue;
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if(aw[t].ol < min_edge) min_edge = aw[t].ol;
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}
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if(av[i].ol < min_edge * o_drop_ratio) to_del_l++;
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}
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if(to_del_l == kv)
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{
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///forward
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to_del_l = 1;
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for (i = 1; i < b_f.n; i++)
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{
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if(check_if_diploid(b_f.a[0], b_f.a[i], g, reverse_sources, miniedgeLen) == 1)
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{
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to_del_l++;
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}
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}
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///backward
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if(to_del_l != kv && b_r.n >= 2)
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{
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to_del_l = 0;
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uint32_t w0, w1;
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w = b_r.a[0];
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kw = get_real_length(g, w, NULL);
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if(kw != 2) goto terminal;
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aw = asg_arc_a(g, w);
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nw = asg_arc_n(g, w);
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for (t = 0; t < nw; t++)
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{
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if(aw[t].del) continue;
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if((aw[t].v>>1) == (v>>1)) continue;
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w0 = aw[t].v;
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}
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to_del_l = 1;
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for (i = 1; i < b_r.n; i++)
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{
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w = b_r.a[i];
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kw = get_real_length(g, w, NULL);
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if(kw != 2) goto terminal;
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aw = asg_arc_a(g, w);
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nw = asg_arc_n(g, w);
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for (t = 0; t < nw; t++)
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{
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if(aw[t].del) continue;
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if((aw[t].v>>1) == (v>>1)) continue;
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w1 = aw[t].v;
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}
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if(check_if_diploid(w0, w1, g, reverse_sources, miniedgeLen) == 1)
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{
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to_del_l++;
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}
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}
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}
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}
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}
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terminal:
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/****************************may have bugs********************************/
|
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@@ -6472,10 +6873,11 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
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if (to_del_l && to_del_r)
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{
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fprintf(stderr, "%.*s\n", Get_NAME_LENGTH((R_INF), v>>1), Get_NAME((R_INF), v>>1));
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for (i = 0; i < nv; ++i)
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{
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if (av[i].del) continue;
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///fprintf(stderr, "%.*s\n", Get_NAME_LENGTH((R_INF), v>>1), Get_NAME((R_INF), v>>1));
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++n_cut;
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av[i].del = 1;
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asg_arc_del(g, av[i].v^1, av[i].ul>>32^1, 1);
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@@ -7856,7 +8258,7 @@ ma_hit_t_alloc* reverse_sources, int id, char* command)
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}
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}
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fflush(stderr);
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}
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@@ -8871,7 +9273,50 @@ int asg_arc_del_orthology_multiple_way(asg_t *g, ma_hit_t_alloc* reverse_sources
|
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||||
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|
||||
int asg_arc_del_chimeric_read(asg_t *g, long long miniedgeLen)
|
||||
{
|
||||
double startTime = Get_T();
|
||||
///the reason is that each read has two direction (query->target, target->query)
|
||||
uint32_t v, v_max, v_maxLen, w, n_vtx = g->n_seq * 2, n_reduced = 0, n_arc;
|
||||
|
||||
for (v = 0; v < n_vtx; ++v)
|
||||
{
|
||||
///if (g->seq_vis[v] != 0) continue;
|
||||
if (g->seq[v>>1].del) continue;
|
||||
if (g->seq[v>>1].c == 0) continue;
|
||||
///fprintf(stderr, "v>>1: %d\n", v>>1);
|
||||
if((get_real_length(g, v, NULL) == 0) || (get_real_length(g, v^1, NULL) == 0))
|
||||
{
|
||||
continue;
|
||||
}
|
||||
|
||||
|
||||
uint32_t convex1, convex2, flag1, flag2;
|
||||
long long l1, l2, ll;
|
||||
flag1 = detect_single_path_with_dels(g, v, &convex1, &l1, NULL);
|
||||
if(flag1 == END_TIPS || flag1 == LONG_TIPS) continue;
|
||||
flag2 = detect_single_path_with_dels(g, v^1, &convex2, &l2, NULL);
|
||||
if(flag2 == END_TIPS || flag2 == LONG_TIPS) continue;
|
||||
ll = l1 + l2 - 1;
|
||||
if(ll <= miniedgeLen)
|
||||
{
|
||||
///fprintf(stderr, "***v>>1: %d\n", v>>1);
|
||||
asg_seq_del(g, v>>1);
|
||||
n_reduced++;
|
||||
}
|
||||
}
|
||||
|
||||
if (n_reduced) {
|
||||
asg_cleanup(g);
|
||||
asg_symm(g);
|
||||
}
|
||||
|
||||
fprintf(stderr, "[M::%s] removed %d chimeric reads\n",
|
||||
__func__, n_reduced);
|
||||
fprintf(stderr, "[M::%s] takes %0.2f s\n\n", __func__, Get_T()-startTime);
|
||||
|
||||
return n_reduced;
|
||||
}
|
||||
|
||||
|
||||
uint32_t detect_single_path_with_dels_by_length
|
||||
@@ -9016,10 +9461,38 @@ long long asg_arc_del_self_circle_untig(asg_t *g, long long circleLen)
|
||||
}
|
||||
|
||||
|
||||
void output_unitig_graph_without_small_bubbles(asg_t *sg, ma_sub_t* coverage_cut,
|
||||
char* output_file_name, long long n_read, long long bubble_dist, long long tipsLen)
|
||||
{
|
||||
asg_cut_tip(sg, tipsLen);
|
||||
asg_pop_bubble(sg, bubble_dist);
|
||||
asg_cut_tip(sg, tipsLen);
|
||||
|
||||
ma_ug_t *ug = NULL;
|
||||
ug = ma_ug_gen(sg);
|
||||
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
|
||||
|
||||
fprintf(stdout, "Writing unitig GFA to disk ...... \n");
|
||||
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
|
||||
sprintf(gfa_name, "%s.no_s_bub.gfa", output_file_name);
|
||||
FILE* output_file = fopen(gfa_name, "w");
|
||||
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
|
||||
fclose(output_file);
|
||||
|
||||
|
||||
sprintf(gfa_name, "%s.simple.no_s_bub.gfa", output_file_name);
|
||||
output_file = fopen(gfa_name, "w");
|
||||
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
|
||||
fclose(output_file);
|
||||
|
||||
free(gfa_name);
|
||||
ma_ug_destroy(ug);
|
||||
}
|
||||
|
||||
|
||||
void output_contig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name, long long n_read, long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long circleLen,
|
||||
ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
|
||||
{
|
||||
|
||||
asg_cut_tip(sg, tipsLen);
|
||||
// asg_pop_bubble(sg, bubble_dist);
|
||||
// asg_arc_del_self_circle_untig(sg, circleLen);
|
||||
@@ -9038,12 +9511,9 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
|
||||
|
||||
cur_cons = sg->n_seq + sg->n_arc;
|
||||
}
|
||||
/**
|
||||
fprintf(stderr, "pop bubbles: %d, sg->n_seq + sg->n_arc: %d\n",
|
||||
asg_pop_bubble(sg, bubble_dist), sg->n_seq + sg->n_arc);
|
||||
fprintf(stderr, "pop bubbles: %d, sg->n_seq + sg->n_arc: %d\n",
|
||||
asg_pop_bubble(sg, bubble_dist), sg->n_seq + sg->n_arc);
|
||||
**/
|
||||
|
||||
asg_arc_identify_simple_bubbles_multi(sg, 1);
|
||||
asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
|
||||
|
||||
///asg_arc_del_self_circle_untig(sg, circleLen);
|
||||
|
||||
@@ -9071,6 +9541,23 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
|
||||
ma_ug_destroy(ug);
|
||||
}
|
||||
|
||||
|
||||
int output_tips(asg_t *g, const All_reads *RNF)
|
||||
{
|
||||
uint32_t v, w, n_vtx = g->n_seq * 2, n_reduced = 0;
|
||||
for (v = 0; v < n_vtx; ++v)
|
||||
{
|
||||
if (g->seq[v>>1].del) continue;
|
||||
|
||||
if(asg_arc_n(g, v) == 0)
|
||||
{
|
||||
fprintf(stderr, "%.*s\n",
|
||||
Get_NAME_LENGTH((*RNF), v>>1),
|
||||
Get_NAME((*RNF), v>>1));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void build_string_graph_without_clean(
|
||||
int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
|
||||
long long n_read, uint64_t* readLen,
|
||||
@@ -9086,24 +9573,21 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
|
||||
}
|
||||
|
||||
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/92668450/ccs",
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/179635219/ccs",
|
||||
// sources, reverse_sources, -1, "init");
|
||||
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/53545052/ccs",
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/130811282/ccs",
|
||||
// sources, reverse_sources, -1, "init");
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
ma_sub_t* coverage_cut;
|
||||
///normalize_ma_hit_t(sources, n_read);
|
||||
normalize_ma_hit_t_single_side(sources, n_read);
|
||||
|
||||
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/92668450/ccs",
|
||||
// sources, reverse_sources, -1, "normalize");
|
||||
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/53545052/ccs",
|
||||
// sources, reverse_sources, -1, "normalize");
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -9119,7 +9603,13 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
|
||||
|
||||
|
||||
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/49678749/ccs",
|
||||
// debug_info_of_specfic_read("m64013_190322_203854/82051959/ccs",
|
||||
// sources, reverse_sources, -1, "clean");
|
||||
|
||||
// debug_info_of_specfic_read("m64013_190322_203854/74385680/ccs",
|
||||
// sources, reverse_sources, -1, "clean");
|
||||
|
||||
// debug_info_of_specfic_read("m64011_190329_072846/80545633/ccs",
|
||||
// sources, reverse_sources, -1, "clean");
|
||||
|
||||
|
||||
@@ -9127,6 +9617,9 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
|
||||
|
||||
|
||||
ma_hit_sub(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
|
||||
|
||||
ma_hit_chimeric(1, sources, reverse_sources, n_read, readLen, coverage_cut);
|
||||
|
||||
ma_hit_cut(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
|
||||
///it seems we do not need ma_hit_flt
|
||||
ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
|
||||
@@ -9136,7 +9629,11 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
|
||||
|
||||
|
||||
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/179635219/ccs",
|
||||
// sources, reverse_sources, -1, "contain");
|
||||
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/130811282/ccs",
|
||||
// sources, reverse_sources, -1, "contain");
|
||||
|
||||
// debug_info_of_specfic_read("m64016_190918_162737/72220752/ccs",
|
||||
// sources, reverse_sources, -1, "contain");
|
||||
@@ -9310,16 +9807,35 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
|
||||
|
||||
asg_arc_del_triangular_directly(sg, MAX_SHORT_TIPS, reverse_sources);
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
///asg_arc_identify_simple_bubbles_multi(sg, 0);
|
||||
// asg_arc_del_chimeric_read(sg, MAX_SHORT_TIPS*2);
|
||||
// asg_cut_tip(sg, MAX_SHORT_TIPS);
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
asg_arc_identify_simple_bubbles_multi(sg, 0);
|
||||
asg_arc_del_orthology_multiple_way(sg, reverse_sources, 0.4, MAX_SHORT_TIPS);
|
||||
asg_cut_tip(sg, MAX_SHORT_TIPS);
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
asg_arc_identify_simple_bubbles_multi(sg, 0);
|
||||
asg_arc_del_too_short_overlaps(sg, 2000, min_ovlp_drop_ratio, reverse_sources, MAX_SHORT_TIPS);
|
||||
asg_cut_tip(sg, MAX_SHORT_TIPS);
|
||||
|
||||
|
||||
|
||||
/**
|
||||
asg_arc_identify_simple_bubbles_multi(sg, 1);
|
||||
asg_arc_del_short_false_link_advance(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
|
||||
**/
|
||||
|
||||
|
||||
|
||||
@@ -9374,9 +9890,17 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
|
||||
// debug_info_of_specfic_node("m64016_190918_162737/141297762/ccs", sg);
|
||||
|
||||
out:
|
||||
///output_tips(sg, &R_INF);
|
||||
|
||||
|
||||
output_unitig_graph(sg, coverage_cut, output_file_name, n_read);
|
||||
output_read_graph(sg, coverage_cut, output_file_name, n_read);
|
||||
|
||||
/****************************may have bugs********************************/
|
||||
output_unitig_graph_without_small_bubbles(sg, coverage_cut, output_file_name, n_read,
|
||||
100000, MAX_SHORT_TIPS);
|
||||
/****************************may have bugs********************************/
|
||||
|
||||
output_contig_graph(sg, coverage_cut, output_file_name, n_read, 10000000, MAX_SHORT_TIPS, 0.1, 20,
|
||||
reverse_sources, MAX_SHORT_TIPS);
|
||||
///output_contig_graph(sg, coverage_cut, output_file_name, n_read, 10000000);
|
||||
|
||||
Reference in New Issue
Block a user