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chhylp123
2022-11-01 21:44:13 -04:00
parent f4b6223fde
commit e66c003b65
6 changed files with 666 additions and 183 deletions
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Overlaps.cpp
+97 -23
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@@ -2693,7 +2693,13 @@ int max_hang, int min_ovlp)
return g;
}
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);
}
asg_t *ma_sg_gen_ul(ma_hit_t_alloc* sources, int64_t n_read, const ma_sub_t *coverage_cut,
R_to_U* ruIndex, int64_t max_hang, int64_t min_ovlp, int64_t ul_occ)
@@ -2705,6 +2711,9 @@ R_to_U* ruIndex, int64_t max_hang, int64_t min_ovlp, int64_t ul_occ)
g->seq[i].c = coverage_cut[i].c;
}
CALLOC(g->seq_vis, (g->n_seq<<1));
// prt_specific_overlap(sources, 22233, 22235, "+");
// prt_specific_overlap(sources, 22235, 22233, "+");
// fprintf(stderr, "[M::%s::] n_read::%ld\n", __func__, n_read);
recover_contain_g(g, sources, ruIndex, max_hang, min_ovlp, ul_occ);
@@ -2712,6 +2721,11 @@ R_to_U* ruIndex, int64_t max_hang, int64_t min_ovlp, int64_t ul_occ)
if(g->seq[i].del) continue;
for (j = 0; j < sources[i].length; j++) {
h = &(sources[i].buffer[j]);
// if((Get_qn(*h) == 22233 && Get_tn(*h) == 22235)||
// (Get_qn(*h) == 22235 && Get_tn(*h) == 22233)) {
// fprintf(stderr, "[M::%s::] qn::%u, tn::%u, del::%u, bl::%u\n", __func__, Get_qn(*h), Get_tn(*h),
// h->del, h->bl);
// }
if(h->del) continue;
r = ma_hit2arc(h, (coverage_cut[Get_qn(*h)].e-coverage_cut[Get_qn(*h)].s),
(coverage_cut[Get_tn(*h)].e-coverage_cut[Get_tn(*h)].s), max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
@@ -10177,8 +10191,52 @@ int asg_cut_internal(asg_t *g, int max_ext)
return cnt;
}
uint32_t reset_weak_ovlp(ma_hit_t_alloc *sc, uint32_t src, uint32_t dst)
{
ma_hit_t_alloc *x = &(sc[src]); uint32_t k, tn; int32_t idx;
for (k = 0; k < x->length; k++) {
if((x->buffer[k].bl&((uint32_t)0x40000000))) continue;
if((x->buffer[k].del)) continue;
tn = Get_tn(x->buffer[k]);
if((Get_ts(x->buffer[k]) == 0) && (Get_te(x->buffer[k]) == Get_READ_LENGTH(R_INF, tn))) {
idx = get_specific_overlap(&(sc[tn]), tn, dst);
if((idx >= 0) && (!(sc[tn].buffer[idx].del)) && (!(sc[tn].buffer[idx].bl&((uint32_t)0x40000000)))) {
return 1;
}
}
}
return 0;
}
static void update_weak_by_contain(void *data, long i, int tid)
{
sset_aux *sl = (sset_aux *)data;
ma_hit_t_alloc *x = &(sl->src[i]);
uint32_t k, qn, tn; int32_t idx;
if(sl->ul_occ == 0) {
for (k = 0; k < x->length; k++) {
if(x->buffer[k].bl&((uint32_t)0x40000000)) x->buffer[k].del = 1;
}
} else if(sl->ul_occ == 1) {
for (k = 0; k < x->length; k++) {
qn = Get_qn(x->buffer[k]);
tn = Get_tn(x->buffer[k]);
if(qn > tn) continue;
if((x->buffer[k].del) && (x->buffer[k].bl&((uint32_t)0x40000000))) {
if(reset_weak_ovlp(sl->src, qn, tn)) {
idx = get_specific_overlap(&(sl->src[tn]), tn, qn);
sl->src[tn].buffer[idx].del = x->buffer[k].del = 0;
}
}
}
} else {
for (k = 0; k < x->length; k++) {
if(x->buffer[k].bl&((uint32_t)0x40000000)) {
x->buffer[k].bl -= ((uint32_t)0x40000000);
}
}
}
}
void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long long num_sources, uint32_t ou_thres)
@@ -10215,27 +10273,36 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
}
}
sset_aux s; s.src = sources; s.ul_occ = 0;
kt_for(asm_opt.thread_num, update_weak_by_contain, &s, num_sources);
for (i = 0; i < num_sources; i++)
{
for (j = 0; j < sources[i].length; j++)
{
if(sources[i].buffer[j].del) continue;
if(sources[i].buffer[j].bl&((uint32_t)0x40000000))
{
sources[i].buffer[j].del = 1;
sources[i].buffer[j].bl -= ((uint32_t)0x40000000);
}
else
{
sources[i].buffer[j].del = 0;
}
}
if(ou_thres != ((uint32_t)-1)) {
s.ul_occ = 1;
kt_for(asm_opt.thread_num, update_weak_by_contain, &s, num_sources);
}
s.ul_occ = 2;
kt_for(asm_opt.thread_num, update_weak_by_contain, &s, num_sources);
// for (i = 0; i < num_sources; i++)
// {
// for (j = 0; j < sources[i].length; j++)
// {
// if(sources[i].buffer[j].del) continue;
// if(sources[i].buffer[j].bl&((uint32_t)0x40000000))
// {
// sources[i].buffer[j].del = 1;
// sources[i].buffer[j].bl -= ((uint32_t)0x40000000);
// }
// else
// {
// sources[i].buffer[j].del = 0;
// }
// }
// }
if(VERBOSE >= 1)
{
fprintf(stderr, "[M::%s] takes %0.2f s\n\n", __func__, Get_T()-startTime);
@@ -31581,13 +31648,15 @@ void rescue_src_ul(ma_hit_t_alloc* src, uint64_t n_read, uint64_t occ)
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)
{
asg_t *sg = NULL;
asg_t *sg = NULL;
// prt_specific_overlap(src, 22233, 22235, "1");
if(ul) rescue_src_ul(src, n_read, UL_COV_THRES);
ma_hit_sub(min_dp, src, n_read, readLen, mini_overlap_length, cov);
detect_chimeric_reads(src, n_read, readLen, *cov, asm_opt.max_ov_diff_final*2.0, ul, UL_COV_THRES);
ma_hit_cut(src, n_read, readLen, mini_overlap_length, cov);
ma_hit_flt(src, n_read, *cov, max_hang_length, mini_overlap_length);
ma_hit_contained_advance(src, n_read, *cov, ruIndex, max_hang_length, mini_overlap_length);
if(!ul) {
sg = ma_sg_gen(src, n_read, *cov, max_hang_length, mini_overlap_length);
asg_arc_del_trans(sg, gap_fuzz);
@@ -31647,12 +31716,17 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
// debug_gfa:;
// }
///should recover edges from sources by using UL alignments
// prt_specific_overlap(sources, 22233, 22235, "0-a");
// prt_specific_overlap(sources, 22235, 22233, "0-a");
if(asm_opt.ar) {
create_ul_info(sources, reverse_sources, max_hang_length, mini_overlap_length, gap_fuzz, min_dp, readLen, coverage_cut, ruIndex,
(asm_opt.max_short_tip*2), 0.15, 3, 0.05, 0.9, &b_mask_t);
}
}
// 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_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,
&b_mask_t, &coverage_cut, asm_opt.ar?&UL_INF:NULL);
// if(asm_opt.ar) exit(1);