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chhylp123
2022-09-23 22:17:38 -04:00
parent f4cc895fa0
commit 38e00d2086
3 changed files with 603 additions and 61 deletions
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Correct.cpp
+73 -46
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@@ -748,41 +748,6 @@ int64_t get_num_wins(int64_t s, int64_t e, int64_t block_s)
nw = (nl/block_s); if((nl%block_s)>0) nw++;
return nw;
}
///[w_s, w_e]
inline int64_t get_win_id_by_s(overlap_region *z, int64_t w_s, int64_t block_s, int64_t *w_e)
{
int64_t n_s = ((z->x_pos_s/block_s)*block_s), wid = (w_s-n_s)/block_s;
if(w_e) {
(*w_e) = n_s + (wid+1)*block_s - 1;
if((*w_e) > z->x_pos_e) (*w_e) = z->x_pos_e;
}
return wid;
}
///[w_s, w_e]
inline int64_t get_win_id_by_e(overlap_region *z, int64_t w_e, int64_t block_s, int64_t *w_s)
{
int64_t n_s = ((z->x_pos_s/block_s)*block_s), wid = (w_e-n_s)/block_s;
if(w_s) {
(*w_s) = n_s + wid*block_s;
if((*w_s) < z->x_pos_s) (*w_s) = z->x_pos_s;
}
return wid;
}
///[w_s, w_e]
inline void get_win_se_by_normalize_xs(overlap_region *z, int64_t norm_w_s, int64_t block_s, int64_t *w_s, int64_t *w_e)
{
int64_t n_s = ((z->x_pos_s/block_s)*block_s), wid = (norm_w_s-n_s)/block_s;
if(w_s) {
(*w_s) = n_s + wid*block_s;
if((*w_s) < z->x_pos_s) (*w_s) = z->x_pos_s;
}
if(w_e) {
(*w_e) = n_s + (wid+1)*block_s - 1;
if((*w_e) > z->x_pos_e) (*w_e) = z->x_pos_e;
}
}
void gen_str_seq(char *dst, int64_t s, int64_t pri_l, uint8_t rev, const ul_idx_t *uref, long long id, int64_t aux_beg, int64_t aux_end)
{
@@ -1297,7 +1262,7 @@ inline double non_trim_error_rate(overlap_region *z, All_reads* rref, const ul_i
return (double)(tErr)/(double)(tLen);
}
inline void append_unmatched_wins(overlap_region *z, int64_t block_s)
void append_unmatched_wins(overlap_region *z, int64_t block_s)
{
int64_t nw, aw = z->w_list.n, k, m, w_id, wn_id, w_s, w_e, idx_e;
nw = get_num_wins(z->x_pos_s, z->x_pos_e+1, block_s);
@@ -1312,7 +1277,7 @@ inline void append_unmatched_wins(overlap_region *z, int64_t block_s)
z->w_list.a[m].cidx = z->w_list.a[m].clen = 0;
z->w_list.a[m].y_start = z->w_list.a[m].y_end = -1;
z->w_list.a[m].error = z->w_list.a[m].error_threshold = -1;
z->w_list.a[m].extra_begin = z->w_list.a[m].extra_end = -1;
z->w_list.a[m].extra_begin = z->w_list.a[m].extra_end = 0;
z->w_list.a[m].x_start = w_e + 1;
wn_id = get_win_id_by_s(z, z->w_list.a[m].x_start, block_s, &w_e);
z->w_list.a[m].x_end = w_e;
@@ -11147,13 +11112,6 @@ char *qstr, kvec_t_u32_warp* q_idx)
return m;///hpc length
}
void inline resize_UC_Read(UC_Read *z, int64_t s)
{
if(z->size < s) {
REALLOC(z->seq, s); z->size = s;
}
}
uint64_t gen_hpc_str(const char *in, uint32_t in_l, UC_Read *z, uint64_t *in_hl)
{
uint64_t hl, k, l;
@@ -12631,10 +12589,78 @@ void ul_lalign_old_ed(overlap_region_alloc* ol, Candidates_list *cl, const ul_id
}
void sub_ciagar_gen(overlap_region *z, uint64_t s, uint64_t e, uint64_t wl)
{
uint64_t qs, qe, sid, eid, k, l, q[2], t[2], mode;
qs = (s/wl)*wl; if(qs < z->x_pos_s) qs = z->x_pos_s; if(qs > z->x_pos_e) return;
qe = (e/wl)*wl; if(qe < e) qe += wl; if(qe > z->x_pos_e+1) qe = z->x_pos_e+1;
sid = get_win_id_by_s(z, qs, wl, NULL);
eid = get_win_id_by_e(z, qe, wl, NULL) + 1;
fprintf(stderr, "***[M::%s] s::%lu, e::%lu, n_qs::%lu, n_qe::%lu, z::[%u, %u)\n",
__func__, s, e, qs, qe, z->x_pos_s, z->x_pos_e+1);
for (k = sid+1, l = sid; k <= eid; k++) {//[sid, eid)
if(k == eid || z->w_list.a[k].extra_end < 0) {
if(k - l > 1 || z->w_list.a[l].extra_end >= 0) {
if(z->w_list.a[l].extra_end < 0) {
if(k < eid) {///global
q[0] = z->w_list.a[l].x_end+1;
t[0] = z->w_list.a[l].y_end+1;
q[1] = z->w_list.a[k-1].x_end+1;
t[1] = z->w_list.a[k-1].y_end+1;
mode = 0;
} else {///forward extension
q[0] = z->w_list.a[l].x_end+1;
t[0] = z->w_list.a[l].y_end+1;
q[1] = qe;
t[1] = z->y_pos_e+1;
mode = 1;
}
} else if(k < eid) {///backward extension
q[0] = qs;
t[0] = z->y_pos_s;
q[1] = z->w_list.a[k-1].x_end+1;
t[1] = z->w_list.a[k-1].y_end+1;
mode = 2;
} else {//semi-global
q[0] = qs; q[1] = qe;
t[0] = t[1] = (uint64_t)-1;
mode = 3;
}
fprintf(stderr, "[M::%s::ql::%lu] qs::%lu, qe::%lu, ts::%lu, te::%lu, mode::%lu\n",
__func__, q[1]-q[0], q[0], q[1], t[0], t[1], mode);
}
l = k;
}
}
}
void cigar_gen(overlap_region *z, ul_ov_t *ov, uint64_t on, uint64_t qn, uint64_t wl)
{
uint64_t i;
for (i = 0; i < on && ov[i].qn == qn; i++) {
sub_ciagar_gen(z, ov[i].qs, ov[i].qe, wl);
}
}
void ul_gap_filling(overlap_region_alloc* ol, kv_ul_ov_t *aln, uint64_t wl)
{
int64_t i, on = ol->length;
for (i = 0; i < on; i++) {
if(ol->list[i].align_length == (uint32_t)-1) continue;
cigar_gen(&(ol->list[i]), aln->a+ol->list[i].align_length, aln->n-ol->list[i].align_length, i, wl);
}
}
void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *uref, char *qstr,
uint64_t ql, UC_Read* qu, UC_Read* tu, Correct_dumy* dumy, bit_extz_t *exz,
haplotype_evdience_alloc* hap, kvec_t_u64_warp* v_idx,
double e_rate, int64_t wl, uint64_t is_base, int64_t sid, void *km)
double e_rate, int64_t wl, kv_ul_ov_t *aln, int64_t sid, void *km)
{
uint64_t i, bs, k, ovl/**, on**/; Window_Pool w; double err;
/**int64_t sc;**/ overlap_region t; overlap_region *z;
@@ -12647,7 +12673,7 @@ void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
bs = (w.window_length)+(THRESHOLD_MAX_SIZE<<1)+1;
resize_UC_Read(tu, bs<<1);
if(is_base) {
if(!aln) {
resize_UC_Read(qu, ql); qu->length = ql; memcpy(qu->seq, qstr, ql);
for (i = 0; i < ol->length; i++) {
z = &(ol->list[i]); ovl = z->x_pos_e+1-z->x_pos_s;
@@ -12685,6 +12711,7 @@ void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
} else {
// fprintf(stderr, "-[M::%s] on::%lu\n", __func__, ol->length);
if(ol->length <= 1) return;
ul_gap_filling(ol, aln, wl);
// for (i = 0; (i < ol->length) && (ol->list[i].is_match == 1); i++); on = i;
// if(on <= 1) return;
// kv_resize(uint64_t, v_idx->a, (on<<1)); v_idx->a.n = on;