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ont simplex support

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chhylp123
2024-11-27 13:27:13 -05:00
parent 80fa5ed436
commit 676385cf8e
10 changed files with 896 additions and 88 deletions
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Overlaps.cpp
+58 -9
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@@ -19,6 +19,7 @@
#include "gfa_ut.h"
#include "assert.h"
#include "khash.h"
#include "ecovlp.h"
KHASH_SET_INIT_INT64(64)
@@ -63,7 +64,6 @@ KRADIX_SORT_INIT(ha_mzl_t_srt1, ha_mzl_t, ha_mzl_t_key, member_size(ha_mzl_t, x)
#define Uc_beg(z) ((uint32_t)((z).a[0]>>32))
#define Uc_end(z) ((uint32_t)((z).a[(z).n-1]>>32)^1)
#define UL_COV_THRES 2
#define PHASE_SEP 64
#define PHASE_SEF 2
#define PHASE_SEP_RATE 0.04
@@ -2969,10 +2969,18 @@ int max_hang, int min_ovlp)
void prt_specific_overlap(ma_hit_t_alloc *src, uint64_t qn, uint64_t tn, const char *cmd)
{
int64_t idx = get_specific_overlap(&(src[qn]), qn, tn);
const ma_hit_t *h = &(src[qn].buffer[idx]);
fprintf(stderr, "%s::idx::%ld[M::%s::] qn::%u, tn::%u, del::%u, bl::%u, ml::%u\n", cmd, idx, __func__,
Get_qn(*h), Get_tn(*h), h->del, h->bl, h->ml);
ma_hit_t *h = NULL; int64_t idx = -1, k;
if(tn != ((uint64_t)-1)) {
idx = get_specific_overlap(&(src[qn]), qn, tn); h = &(src[qn].buffer[idx]);
fprintf(stderr, "%s::idx::%ld[M::%s::] qn::%u, tn::%u, del::%u, bl::%u, ml::%u\n", cmd, idx, __func__,
Get_qn(*h), Get_tn(*h), h->del, h->bl, h->ml);
} else {
for (k = 0; k < src[qn].length; k++) {
h = &(src[qn].buffer[k]);
fprintf(stderr, "%s::idx::%ld[M::%s::] qn::%u, tn::%u, del::%u, bl::%u, ml::%u\n", cmd, idx, __func__,
Get_qn(*h), Get_tn(*h), h->del, h->bl, h->ml);
}
}
}
asg_t *ma_sg_gen_ul(ma_hit_t_alloc* sources, int64_t n_read, const ma_sub_t *coverage_cut,
@@ -5667,8 +5675,12 @@ long long weakID, uint32_t w_qs, uint32_t w_qe)
{
strongID = Get_tn(aim_paf->buffer[i]);
index = get_specific_overlap(&(reverse_paf_list[strongID]), strongID, weakID);
if(index != -1)
{
if(index != -1) {
// if((Get_qn(aim_paf->buffer[i]) == 27087 && weakID == 27128) || (Get_qn(aim_paf->buffer[i]) == 27128 && weakID == 27087)) {
// ma_hit_t *h = &(aim_paf->buffer[i]);
// fprintf(stderr, "[M::%s]\t%.*s(qn::%u)\t%u\t%u\t%u\t%c\t%.*s(tn::%u)\t%u\t%u\t%u\t%u\t%u\t255\n", __func__, (int)Get_NAME_LENGTH(R_INF, Get_qn(*h)), Get_NAME((R_INF), Get_qn(*h)), Get_qn(*h), (uint32_t)Get_READ_LENGTH(R_INF, Get_qn(*h)), Get_qs(*h), Get_qe(*h), "+-"[h->rev],
// (int)Get_NAME_LENGTH(R_INF, Get_tn(*h)), Get_NAME((R_INF), Get_tn(*h)), Get_tn(*h), (uint32_t)Get_READ_LENGTH(R_INF, Get_tn(*h)), Get_ts(*h), Get_te(*h), h->ml, h->bl);
// }
return 0;
}
}
@@ -11193,6 +11205,11 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
index = get_specific_overlap(&(sources[tn]), tn, qn);
// if(index < 0 || index >= sources[tn].length) fprintf(stderr, "sb, tn: %u, qn: %u, index: %ld, length: %u\n", tn, qn, index, sources[tn].length);
sources[tn].buffer[index].bl |= ((uint32_t)0x40000000);
// ma_hit_t *h = &(sources[i].buffer[j]);
// if((Get_qn(*h) == 27087 && Get_tn(*h) == 27128) || (Get_tn(*h) == 27087 && Get_qn(*h) == 27128)) {
// fprintf(stderr, "[M::%s]\t%.*s(qn::%u)\t%u\t%u\t%u\t%c\t%.*s(tn::%u)\t%u\t%u\t%u\t%u\t%u\t255\n", __func__, (int)Get_NAME_LENGTH(R_INF, Get_qn(*h)), Get_NAME((R_INF), Get_qn(*h)), Get_qn(*h), (uint32_t)Get_READ_LENGTH(R_INF, Get_qn(*h)), Get_qs(*h), Get_qe(*h), "+-"[h->rev],
// (int)Get_NAME_LENGTH(R_INF, Get_tn(*h)), Get_NAME((R_INF), Get_tn(*h)), Get_tn(*h), (uint32_t)Get_READ_LENGTH(R_INF, Get_tn(*h)), Get_ts(*h), Get_te(*h), h->ml, h->bl);
// }
}
}
}
@@ -38528,17 +38545,43 @@ void prt_dbg_gfa(asg_t *sg, const char *suffix, ma_sub_t *cov, ma_hit_t_alloc* s
free(gfa_name); free(o_file);
}
void prt_dbg_rid_ovlp(ma_hit_t_alloc *ov, int64_t rid, char *rn, const char *cmd)
{
uint64_t k; ma_hit_t *h = NULL;
if(rid < 0) {
for (k = 0; k < R_INF.total_reads; k++) {
if (memcmp(rn, Get_NAME((R_INF), k), Get_NAME_LENGTH((R_INF), k)) == 0) break;
}
if(k >= R_INF.total_reads) return;
rid = k;
}
fprintf(stderr, "\n[M::%s::%s::id::%ld]\n", __func__, cmd, rid);
for (k = 0; k < ov[rid].length; k++) {
h = &(ov[rid].buffer[k]);
if(h->del) continue;
fprintf(stderr, "%.*s(qn::%u)\t%u\t%u\t%u\t%c\t%.*s(tn::%u)\t%u\t%u\t%u\t%u\t%u\t255\n", (int)Get_NAME_LENGTH(R_INF, Get_qn(*h)), Get_NAME((R_INF), Get_qn(*h)), Get_qn(*h), (uint32_t)Get_READ_LENGTH(R_INF, Get_qn(*h)), Get_qs(*h), Get_qe(*h), "+-"[h->rev],
(int)Get_NAME_LENGTH(R_INF, Get_tn(*h)), Get_NAME((R_INF), Get_tn(*h)), Get_tn(*h), (uint32_t)Get_READ_LENGTH(R_INF, Get_tn(*h)), Get_ts(*h), Get_te(*h), h->ml, h->bl);
}
}
asg_t *gen_init_sg(int32_t min_dp, uint64_t n_read, int64_t mini_overlap_length, int64_t max_hang_length, int64_t gap_fuzz,
ma_hit_t_alloc* src, uint64_t* readLen, R_to_U* ruIndex, bub_label_t *b_mask_t, ma_sub_t** cov, all_ul_t *ul, telo_end_t *te)
{
asg_t *sg = NULL;
// prt_specific_overlap(src, 22233, 22235, "1");
// prt_dbg_rid_ovlp(src, 3700, NULL, "1");
if(ul) rescue_src_ul(src, n_read, UL_COV_THRES);
// prt_dbg_rid_ovlp(src, 3700, NULL, "2");
ma_hit_sub(min_dp, src, n_read, readLen, mini_overlap_length, cov);
// prt_dbg_rid_ovlp(src, 3700, NULL, "3");
detect_chimeric_reads(src, n_read, readLen, *cov, asm_opt.max_ov_diff_final*2.0, ul, UL_COV_THRES);
// prt_dbg_rid_ovlp(src, 3700, NULL, "4");
ma_hit_cut(src, n_read, readLen, mini_overlap_length, cov);
// prt_dbg_rid_ovlp(src, 3700, NULL, "5");
ma_hit_flt(src, n_read, *cov, max_hang_length, mini_overlap_length);
// prt_dbg_rid_ovlp(src, 3700, NULL, "6");
ma_hit_contained_advance(src, n_read, *cov, ruIndex, max_hang_length, mini_overlap_length);
// prt_dbg_rid_ovlp(src, 3700, NULL, "7");
if(!ul) {
sg = ma_sg_gen(src, n_read, *cov, max_hang_length, mini_overlap_length);
@@ -38650,6 +38693,8 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
///just for debug
renew_graph_init(sources, reverse_sources, sg, coverage_cut, ruIndex, n_read);
// if(asm_opt.is_ont) handle_chemical_arc(asm_opt.thread_num, R_INF.total_reads);
// if(asm_opt.is_ont) handle_chemical_r(asm_opt.thread_num, R_INF.total_reads);
///it's hard to say which function is better
///normalize_ma_hit_t_single_side(sources, n_read);
@@ -38681,7 +38726,9 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
// prt_specific_overlap(sources, 22233, 22235, "0-b");
// prt_specific_overlap(sources, 22235, 22233, "0-b");
clean_weak_ma_hit_t(sources, reverse_sources, n_read, asm_opt.ar?UL_COV_THRES:(uint32_t)-1);
// prt_dbg_rid_ovlp(sources, 27087, NULL, "0-a");
if(!(asm_opt.is_ont)) clean_weak_ma_hit_t(sources, reverse_sources, n_read, asm_opt.ar?UL_COV_THRES:(uint32_t)-1);
// prt_dbg_rid_ovlp(sources, 27087, NULL, "0-b");
// prt_specific_overlap(sources, 22233, 22235, "0-c");
// prt_specific_overlap(sources, 22235, 22233, "0-c");
sg = gen_init_sg(min_dp, n_read, mini_overlap_length, max_hang_length, gap_fuzz, sources, readLen, ruIndex,
@@ -39006,7 +39053,9 @@ long long bubble_dist, int read_graph, int write)
if (!(asm_opt.flag & HA_F_BAN_ASSEMBLY))
{
if(asm_opt.is_ont) handle_chemical_r(asm_opt.thread_num, R_INF.total_reads);
try_rescue_overlaps(sources, reverse_sources, n_read, 4);
clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length,
max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 0);