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update 0.14-r310

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chhylp123
2021-02-13 23:21:45 -05:00
parent 5bb22f701c
commit 18086e2c2e
6 changed files with 1329 additions and 175 deletions
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hic.cpp
+5 -127
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@@ -7369,7 +7369,7 @@ void init_chain_hic_warp(ma_ug_t* ug, hc_links* link, bubble_type* bub, chain_hi
}
}
fprintf(stderr, "# chain: %u, # pre chain: %u\n", m, (uint32_t)(*c_w).n);
///fprintf(stderr, "# chain: %u, # pre chain: %u\n", m, (uint32_t)(*c_w).n);
(*c_w).n = m;
for (i = 0; i < (*c_w).n; i++)
{
@@ -11272,7 +11272,7 @@ int alignment_worker_pipeline(sldat_t* sl, const enzyme *fn1, const enzyme *fn2)
kt_pipeline(3, worker_pipeline, sl, 3);
fprintf(stderr, "fn1->a[i]: %s, fn2->a[i]: %s, sl->hits.a.n: %u\n", fn1->a[i], fn2->a[i], (uint32_t)sl->hits.a.n);
///fprintf(stderr, "fn1->a[i]: %s, fn2->a[i]: %s, sl->hits.a.n: %u\n", fn1->a[i], fn2->a[i], (uint32_t)sl->hits.a.n);
kseq_destroy(sl->ks1);
@@ -11281,11 +11281,11 @@ int alignment_worker_pipeline(sldat_t* sl, const enzyme *fn1, const enzyme *fn2)
gzclose(fp2);
}
fprintf(stderr, "+sl->hits.a.n: %u\n", (uint32_t)sl->hits.a.n);
///fprintf(stderr, "+sl->hits.a.n: %u\n", (uint32_t)sl->hits.a.n);
dedup_hits(&(sl->hits));
fprintf(stderr, "-sl->hits.a.n: %u\n", (uint32_t)sl->hits.a.n);
///fprintf(stderr, "-sl->hits.a.n: %u\n", (uint32_t)sl->hits.a.n);
return 1;
}
@@ -11401,127 +11401,6 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
return 1;
}
int hic_short_align_back(const char *fn1, const char *fn2, ha_ug_index* idx)
{
double index_time = yak_realtime();
sldat_t sl;
gzFile fp1, fp2;
kvec_hc_edge back_hc_edge;
kv_init(back_hc_edge.a);
if ((fp1 = gzopen(fn1, "r")) == 0) return 0;
if ((fp2 = gzopen(fn2, "r")) == 0) return 0;
sl.ks1 = kseq_init(fp1);
sl.ks2 = kseq_init(fp2);
sl.idx = idx;
sl.link = idx->link;
sl.chunk_size = 20000000;
sl.n_thread = asm_opt.thread_num;
sl.total_base = sl.total_pair = 0;
idx->max_cnt = 5;
kv_init(sl.hits.a);
if(!load_hc_hits(&sl.hits, asm_opt.output_file_name))
{
/*******************************for debug************************************/
// load_reads(&R1, fn1);
// test_reads(&R1, fn1);
// load_reads(&R2, fn2);
// test_reads(&R1, fn1);
/*******************************for debug************************************/
fprintf(stderr, "+sl->hits.a.n: %u\n", (uint32_t)sl.hits.a.n);
kt_pipeline(3, worker_pipeline, &sl, 3);
fprintf(stderr, "-sl->hits.a.n: %u\n", (uint32_t)sl.hits.a.n);
fprintf(stderr, "fn1: %s, fn2: %s\n", fn1, fn2);
/*******************************for debug************************************/
// sort_hits(&sl.hits);
// print_hits(idx, &sl.hits, fn1);
/*******************************for debug************************************/
dedup_hits(&sl.hits);
write_hc_hits(&sl.hits, asm_opt.output_file_name);
}
fprintf(stderr, "u.n: %d, uID_bits: %lu, pos_bits: %lu, sl.hits.a.n: %u\n", (uint32_t)idx->ug->u.n, idx->uID_bits, idx->pos_bits, (uint32_t)sl.hits.a.n);
H_partition hap;
MT M;
init_MT(&M, idx->ug->g->n_seq<<1);
bubble_type bub;
memset(&bub, 0, sizeof(bubble_type));
bub.round_id = 0; bub.n_round = 2;
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
identify_bubbles(idx->ug, &bub, idx->link);
if(bub.round_id == 0)
{
collect_hc_links(sl.idx, &sl.hits, idx->link, &bub, &M);
collect_hc_reverse_links(idx->link, idx->ug, &bub);
}
init_hic_p((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub, &back_hc_edge, &M, &hap, 0);
///init_hic_p_new((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub, &back_hc_edge, &M);
reset_H_partition(&hap, (bub.round_id == 0? 1 : 0));
init_contig_partition(&hap, idx, &bub);
phasing_improvement(&hap, &(hap.g_p), idx, &bub);
label_unitigs(&(hap.g_p), idx->ug);
///print_hc_links(idx->link, 0, &hap);
}
cluster_contigs(&bub, idx, &sl.hits, &M, &hap);
destory_MT(&M);
///print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, idx->link, idx);
///print_hits(idx, &sl.hits, fn1);
///print_debug_bubble_graph(&bub, idx->ug, asm_opt.output_file_name);
// print_bubble_chain(&bub);
// print_hc_links(idx->link, 0, &hap);
///print_contig_partition(&hap, "final");
// uint32_t i;
// for (i = 0; i < idx->ug->g->n_seq; i++)
// {
// fprintf(stderr, "utg%.6ul, index: %u\n", (int)(i+1), bub.index[i]);
// }
destory_contig_partition(&hap);
kv_destroy(back_hc_edge.a);
return 1;
/*******************************for debug************************************/
// destory_reads(&R1);
// destory_reads(&R2);
/*******************************for debug************************************/
print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, idx->link, idx);
collect_hc_reverse_links(idx->link, idx->ug, &bub);
normalize_hc_links(idx->link);
/*******************************for debug************************************/
///print_hc_links(&link);
/*******************************for debug************************************/
min_cut_t* cut = clean_hap(idx->link, &bub, idx->ug);
///print_bubbles(idx->ug, &bub, NULL, &link, idx);
G_partition* gp = clean_bubbles(idx->link, &bub, cut, idx->ug);
///print_hc_links(&link);
destory_min_cut_t(cut); free(cut);
destory_G_partition(gp); free(gp);
kv_destroy(sl.hits.a);
destory_bubbles(&bub);
kseq_destroy(sl.ks1);
kseq_destroy(sl.ks2);
gzclose(fp1);
gzclose(fp2);
fprintf(stderr, "[M::%s::%.3f] processed %lu pairs; %lu bases\n", __func__, yak_realtime()-index_time, sl.total_pair, sl.total_base);
return 1;
}
void hic_analysis(ma_ug_t *ug, asg_t* read_g, hc_links* link)
{
@@ -11533,8 +11412,7 @@ void hic_analysis(ma_ug_t *ug, asg_t* read_g, hc_links* link)
ug_index->read_g = read_g;
ug_index->link = link;
///test_unitig_index(ug_index, ug);
///hic_short_align(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index);
hic_short_align_back(asm_opt.hic_reads[0]->a[0], asm_opt.hic_reads[1]->a[0], ug_index);
hic_short_align(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index);
destory_hc_pt_index(ug_index);
}