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cal_exz_infi

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chhylp123
2022-09-24 16:16:54 -04:00
parent 38e00d2086
commit a297105258
3 changed files with 246 additions and 48 deletions
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Correct.cpp
+224 -37
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@@ -11262,7 +11262,8 @@ void prt_cigar(uint16_t *ca, uint32_t cn)
inline uint32_t gen_backtrace_adv_exz(window_list *p, overlap_region *z, All_reads *rref, hpc_t *hpc_g, const ul_idx_t *uref, inline uint32_t gen_backtrace_adv_exz(window_list *p, overlap_region *z, All_reads *rref, hpc_t *hpc_g, const ul_idx_t *uref,
char *qstr, char *tstr, bit_extz_t *exz, uint32_t rev, uint32_t id) char *qstr, char *tstr, bit_extz_t *exz, uint32_t rev, uint32_t id)
{ {
int64_t qs, qe, ql, tl, aln_l, t_pri_l, thres, ts; if(p->error < 0 || p->y_end < 0) return 0;
int64_t qs, qe, ql, tl, aln_l, t_pri_l, thres, ts, t_tot_l;
int64_t aux_beg, aux_end; int64_t aux_beg, aux_end;
char *q_string, *t_string; char *q_string, *t_string;
///there is no problem for x ///there is no problem for x
@@ -11272,7 +11273,16 @@ char *qstr, char *tstr, bit_extz_t *exz, uint32_t rev, uint32_t id)
///y_start is the real y_start ///y_start is the real y_start
///for the window with cigar, y_start has already reduced extra_begin ///for the window with cigar, y_start has already reduced extra_begin
ts = p->y_start; aux_beg = p->extra_begin; aux_end = p->extra_end; ts = p->y_start; aux_beg = p->extra_begin; aux_end = p->extra_end;
t_pri_l = aln_l - aux_beg - aux_end; if(aux_end >= 0) {
t_pri_l = aln_l - aux_beg - aux_end;
} else {
if(hpc_g) t_tot_l = hpc_len(*hpc_g, id);
else if(uref) t_tot_l = uref->ug->u.a[id].len;
else t_tot_l = Get_READ_LENGTH((*rref), id);
t_pri_l = ts + aln_l - aux_beg; if(t_pri_l > t_tot_l) t_pri_l = t_tot_l;
t_pri_l = t_pri_l - ts;
}
q_string = qstr + qs; tl = t_pri_l; q_string = qstr + qs; tl = t_pri_l;
if(rref) { if(rref) {
@@ -12588,70 +12598,247 @@ void ul_lalign_old_ed(overlap_region_alloc* ol, Candidates_list *cl, const ul_id
} }
} }
inline uint64_t scale_ed_thre(uint32_t err)
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; uint64_t bd = (err<<1)+1, w;
w = (bd>>bitw); w <<= bitw; if(w < bd) w += bitwbit;
err = (w-1)>>1; if(err > MAX_E) err = MAX_E;
return err;
}
///[qs, qe)
int64_t update_semi_coord(const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref, overlap_region *z,
int64_t qs, int64_t qe, int64_t thre, int64_t *ts, int64_t *te, int64_t *aux_beg)
{
int64_t ql = qe - qs, aln_l, t_tot_l, id = z->y_id, aux_end, tl;
(*ts) = (qs - z->x_pos_s) + z->y_pos_s;
(*ts) += y_start_offset(qs, &(z->f_cigar));
aln_l = ql + (thre<<1);
if(hpc_g) t_tot_l = hpc_len(*hpc_g, id);
else if(uref) t_tot_l = uref->ug->u.a[id].len;
else t_tot_l = Get_READ_LENGTH((*rref), id);
if(!init_waln(thre, (*ts), t_tot_l, aln_l, aux_beg, &aux_end, ts, &tl)) {
(*ts) = (*te) = (*aux_beg) = -1;
return 0;
}
(*te) = (*ts) + tl;
return 1;
}
int64_t cal_exz_infi(overlap_region *z, const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref, bit_extz_t *exz, char* qstr, UC_Read *tu, int64_t qs, int64_t qe, int64_t ts, int64_t te, int64_t thre, int64_t mode)
{
int64_t aux_beg = 0, bd = (((thre)<<1)+1), ql, tl, t_tot_l = -1; int32_t nword = ((bd>>bitw)+(!!(bd&bitz)));
char *q_string, *t_string; int32_t rev = z->y_pos_strand, id = z->y_id; ql = qe - qs;
if(mode == 3) {
update_semi_coord(uref, hpc_g, rref, z, qs, qe, thre, &ts, &te, &aux_beg);
} else if(mode == 2) {
ts = te - ql - thre; if(ts < 0) ts = 0;
} else if(mode == 1) {
te = ts + ql + thre;
if(hpc_g) t_tot_l = hpc_len(*hpc_g, id);
else if(uref) t_tot_l = uref->ug->u.a[id].len;
else t_tot_l = Get_READ_LENGTH((*rref), id);
if(te > t_tot_l) te = t_tot_l;
}
if((qe > qs) && (te > ts) && (ts != -1) && (te != -1)) {
ql = qe - qs; q_string = qstr + qs;
tl = te - ts; resize_UC_Read(tu, tl);
// fprintf(stderr, "q::[%ld, %ld), t::[%ld, %ld), thre::%ld, t_tot_l::%ld\n", qs, qe, ts, te, thre, t_tot_l);
if(rref) {
recover_UC_Read_sub_region(tu->seq, ts, tl, rev, rref, id); t_string = tu->seq;
} else {
t_string = return_str_seq_exz(tu->seq, ts, tl, rev, hpc_g, uref, id);
}
clear_align(*exz);
// fprintf(stderr, ", nword::%d", nword);
// if(ql < 0) fprintf(stderr, "qs::%ld, qe::%ld\n", qs, qe);
// return 0;
if(nword <= 1) {
if(mode == 0) { //global
ed_band_cal_global_64_w_trace(t_string, tl, q_string, ql, thre, exz);
} else if(mode == 1) {///forward extension
// fprintf(stderr, "q::[%ld, %ld), t::[%ld, %ld), thre::%ld\n", qs, qe, ts, te, thre);
ed_band_cal_extension_64_0_w_trace(t_string, tl, q_string, ql, thre, exz);
} else if(mode == 2) {///backward extension
ed_band_cal_extension_64_1_w_trace(t_string, tl, q_string, ql, thre, exz);
} else if(mode == 3) {//semi-global
ed_band_cal_semi_64_w_absent_diag_trace(t_string, tl, q_string, ql, thre, aux_beg, exz);
}
} else if(nword == 2) {
if(mode == 0) { //global
ed_band_cal_global_128_w_trace(t_string, tl, q_string, ql, thre, exz);
} else if(mode == 1) {///forward extension
ed_band_cal_extension_128_0_w_trace(t_string, tl, q_string, ql, thre, exz);
} else if(mode == 2) {///backward extension
ed_band_cal_extension_128_1_w_trace(t_string, tl, q_string, ql, thre, exz);
} else if(mode == 3) {//semi-global
ed_band_cal_semi_128_w_absent_diag_trace(t_string, tl, q_string, ql, thre, aux_beg, exz);
}
} else {
if(mode == 0) { //global
ed_band_cal_global_infi_w_trace(t_string, tl, q_string, ql, thre, &nword, exz);
} else if(mode == 1) {///forward extension
ed_band_cal_extension_infi_0_w_trace(t_string, tl, q_string, ql, thre, &nword, exz);
} else if(mode == 2) {///backward extension
ed_band_cal_extension_infi_1_w_trace(t_string, tl, q_string, ql, thre, &nword, exz);
} else if(mode == 3) {//semi-global
ed_band_cal_semi_infi_w_absent_diag_trace(t_string, tl, q_string, ql, thre, aux_beg, &nword, exz);
}
}
if(is_align(*exz)) {
return 1;
}
return 0;
}
return 0;
}
void hc_aln_exz(overlap_region *z, const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref,
char* qstr, UC_Read *tu, int64_t qs, int64_t qe, int64_t ts, int64_t te, int64_t estimate_err,
int64_t mode, int64_t wl, bit_extz_t *exz, double e_rate)
{
int64_t thre, ql = qe - qs, thre0;
if(((ts == -1) && (te == -1))) mode = 3;///set to semi-global
// fprintf(stderr, "[M::%s::ql::%ld] qs::%ld, qe::%ld, ts::%ld, te::%ld, mode::%ld, estimate_err::%ld, e_rate::%f",
// __func__, ql, qs, qe, ts, te, mode, estimate_err, e_rate);
if(ql <= MAX_L) {
thre = scale_ed_thre(estimate_err); if(thre > ql) thre = ql;
if(cal_exz_infi(z, uref, hpc_g, rref, exz, qstr, tu, qs, qe, ts, te, thre, mode)) {
// fprintf(stderr, ", err::%d, thre::%d, scale::%ld(+)\n", exz->err, exz->thre, thre);
return;
}
thre0 = thre; thre = ql*e_rate;
thre = scale_ed_thre(thre); if(thre > ql) thre = ql;
if(thre > thre0) {
if(cal_exz_infi(z, uref, hpc_g, rref, exz, qstr, tu, qs, qe, ts, te, thre, mode)) {
// fprintf(stderr, ", err::%d, thre::%d, scale::%ld(-)\n", exz->err, exz->thre, thre);
return;
}
}
thre0 = thre; thre <<= 1;
thre = scale_ed_thre(thre); if(thre > ql) thre = ql;
if(thre > thre0) {
if(cal_exz_infi(z, uref, hpc_g, rref, exz, qstr, tu, qs, qe, ts, te, thre, mode)) {
// fprintf(stderr, ", err::%d, thre::%d, scale::%ld(-)\n", exz->err, exz->thre, thre);
return;
}
}
thre0 = thre; thre = ql*0.51;
thre = scale_ed_thre(thre); if(thre > ql) thre = ql;
if(thre > thre0) {
if(cal_exz_infi(z, uref, hpc_g, rref, exz, qstr, tu, qs, qe, ts, te, thre, mode)) {
// fprintf(stderr, ", err::%d, thre::%d, scale::%ld(-)\n", exz->err, exz->thre, thre);
return;
}
}
// fprintf(stderr, ", err::%d, thre::%d\n", INT32_MAX, exz->thre);
}
}
void sub_ciagar_gen(overlap_region *z, uint64_t s, uint64_t e, uint64_t wl,
const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref, char* qstr, UC_Read *tu, bit_extz_t *exz, double e_rate)
{
uint64_t qs, qe, sid, eid, k, l, m, tot_e, c_e; int64_t 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; 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; qe = (e/wl)*wl; if(qe < e) qe += wl; if(qe > z->x_pos_e+1) qe = z->x_pos_e+1;
if(qe <= 0) return;
sid = get_win_id_by_s(z, qs, wl, NULL); sid = get_win_id_by_s(z, qs, wl, NULL);
eid = get_win_id_by_e(z, qe, wl, NULL) + 1; eid = get_win_id_by_e(z, qe-1, wl, NULL) + 1;///must qe-1 instead of qe!!!!!!
fprintf(stderr, "***[M::%s] s::%lu, e::%lu, n_qs::%lu, n_qe::%lu, z::[%u, %u)\n", if(sid >= eid) return;
__func__, s, e, qs, qe, z->x_pos_s, z->x_pos_e+1); // fprintf(stderr, "***[M::%s] s::%lu, e::%lu, n_qs::%lu, n_qe::%lu, z::[%u, %u), sid::%lu, eid::%lu, w_list.n::%lu\n",
// __func__, s, e, qs, qe, z->x_pos_s, z->x_pos_e+1, sid, eid, (uint64_t)z->w_list.n);
for (k = sid+1, l = sid; k <= eid; k++) {//[sid, eid) for (k = sid+1, l = sid; k <= eid; k++) {//[sid, eid)
if(k == eid || z->w_list.a[k].extra_end < 0) { if(k == eid || z->w_list.a[k].extra_end < 0) {
if(k - l > 1 || z->w_list.a[l].extra_end >= 0) { if(k - l > 1 || z->w_list.a[l].extra_end >= 0) {
q[0] = q[1] = t[0] = t[1] = -1; mode = -1; tot_e = 0;
if(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;
q[0] = z->w_list.a[l].x_end+1; if(z->w_list.a[l].y_end != -1) {
t[0] = z->w_list.a[l].y_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 } else {///first window
q[0] = qs; q[0] = qs;
t[0] = z->y_pos_s; if(z->w_list.a[l].y_end != -1) {
q[1] = z->w_list.a[k-1].x_end+1; c_e = z->w_list.a[l].error;
t[1] = z->w_list.a[k-1].y_end+1; } else {
mode = 2; c_e = z->w_list.a[l].x_end + 1 - z->w_list.a[l].x_start;
} else {//semi-global if(c_e > THRESHOLD_MAX_SIZE) c_e = THRESHOLD_MAX_SIZE;
q[0] = qs; q[1] = qe; }
t[0] = t[1] = (uint64_t)-1; tot_e += c_e;
mode = 3;
} }
fprintf(stderr, "[M::%s::ql::%lu] qs::%lu, qe::%lu, ts::%lu, te::%lu, mode::%lu\n", if(k > sid && k < eid && z->w_list.a[k].extra_end < 0) {
__func__, q[1]-q[0], q[0], q[1], t[0], t[1], mode); q[1] = z->w_list.a[k-1].x_end+1;
if(z->w_list.a[k].y_end != -1) {
// if(z->w_list.a[k-1].y_end == -1) {
// fprintf(stderr, "[M::%s::rid::%lu] k::%lu, sid::%lu, eid::%lu, k_y_end::%d, k-1_y_end::%d, xk[%d, %d)\n",
// __func__, rid, k, sid, eid, z->w_list.a[k].y_end, z->w_list.a[k-1].y_end,
// z->w_list.a[k].x_start, z->w_list.a[k].x_end+1);
// }
assert(z->w_list.a[k-1].y_end != -1);
t[1] = z->w_list.a[k-1].y_end+1;
}
} else {///last window
q[1] = qe;
}
if((t[0] != -1) && (t[1] != -1)) {
mode = 0;//global
} else if((t[0] != -1) && (t[1] == -1)) {
/**t[1] = z->y_pos_e+1;**/ mode = 1;///forward extension
} else if((t[0] == -1) && (t[1] != -1)) {
/**t[0] = z->y_pos_s;**/ mode = 2;///backward extension
} else {
mode = 3;//semi-global
}
for (m = l+1; m < k; m++) {
if(z->w_list.a[m].y_end != -1) {
c_e = z->w_list.a[m].error;
} else {
c_e = z->w_list.a[m].x_end + 1 - z->w_list.a[m].x_start;
if(c_e > THRESHOLD_MAX_SIZE) c_e = THRESHOLD_MAX_SIZE;
}
tot_e += c_e;
}
// if(q[1] < q[0]) {
// fprintf(stderr, "[M::%s::ql::%lu] qs::%lu, qe::%lu, ts::%lu, te::%lu, mode::%ld, tot_e::%lu\n",
// __func__, q[1]-q[0], q[0], q[1], t[0], t[1], mode, tot_e);
// }
hc_aln_exz(z, uref, hpc_g, rref, qstr, tu, q[0], q[1], t[0], t[1], tot_e, mode, wl, exz, e_rate);
} }
l = k; l = k;
} }
} }
} }
void cigar_gen(overlap_region *z, ul_ov_t *ov, uint64_t on, uint64_t qn, uint64_t wl) void cigar_gen(overlap_region *z, ul_ov_t *ov, uint64_t on, uint64_t qn, uint64_t wl,
const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref, char* qstr, UC_Read *tu, bit_extz_t *exz, double e_rate)
{ {
uint64_t i; uint64_t i;
for (i = 0; i < on && ov[i].qn == qn; i++) { for (i = 0; i < on && ov[i].qn == qn; i++) {
sub_ciagar_gen(z, ov[i].qs, ov[i].qe, wl); sub_ciagar_gen(z, ov[i].qs, ov[i].qe, wl, uref, hpc_g, rref, qstr, tu, exz, e_rate);
} }
} }
void ul_gap_filling(overlap_region_alloc* ol, kv_ul_ov_t *aln, uint64_t wl) void ul_gap_filling(overlap_region_alloc* ol, kv_ul_ov_t *aln, uint64_t wl,
const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref, char* qstr, UC_Read *tu, bit_extz_t *exz, double e_rate)
{ {
int64_t i, on = ol->length; int64_t i, on = ol->length;
for (i = 0; i < on; i++) { for (i = 0; i < on; i++) {
if(ol->list[i].align_length == (uint32_t)-1) continue; 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); cigar_gen(&(ol->list[i]), aln->a+ol->list[i].align_length, aln->n-ol->list[i].align_length, i, wl,
uref, hpc_g, rref, qstr, tu, exz, e_rate);
} }
} }
@@ -12711,7 +12898,7 @@ void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
} else { } else {
// fprintf(stderr, "-[M::%s] on::%lu\n", __func__, ol->length); // fprintf(stderr, "-[M::%s] on::%lu\n", __func__, ol->length);
if(ol->length <= 1) return; if(ol->length <= 1) return;
ul_gap_filling(ol, aln, wl); ul_gap_filling(ol, aln, wl, uref, NULL, NULL, qu->seq, tu, exz, err);
// for (i = 0; (i < ol->length) && (ol->list[i].is_match == 1); i++); on = i; // for (i = 0; (i < ol->length) && (ol->list[i].is_match == 1); i++); on = i;
// if(on <= 1) return; // if(on <= 1) return;
// kv_resize(uint64_t, v_idx->a, (on<<1)); v_idx->a.n = on; // kv_resize(uint64_t, v_idx->a, (on<<1)); v_idx->a.n = on;
Levenshtein_distance.h
+9 -1
View File
@@ -537,6 +537,9 @@ inline uint32_t pop_trace(asg16_v *res, uint32_t i, uint16_t *c, uint32_t *len)
return i; return i;
} }
///511 -> 16 64-bits
#define MAX_E 511
#define MAX_L 2500
typedef uint64_t w_sig; typedef uint64_t w_sig;
#define bitw (6) #define bitw (6)
@@ -3354,7 +3357,9 @@ inline void ed_band_cal_extension_64_0_w_trace(char *pstr, int32_t pn, char *tst
c = seq_nt4_table[(uint8_t)pstr[i_bd]]; c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm; if(c < 4) Peq[c] |= mm;
} }
// if(((ez->path.n+5)>(ez->nword*tn*5))||((ez->path.n+5)>(ez->path.m))) {
// fprintf(stderr, "[M::%s::] pn::%d, tn::%d\n", __func__, pn, tn);
// }
ez->path.a[ez->path.n++] = D0;//diff ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff ez->path.a[ez->path.n++] = VN;//diff
@@ -3365,6 +3370,9 @@ inline void ed_band_cal_extension_64_0_w_trace(char *pstr, int32_t pn, char *tst
if (!(D0&(1ULL))) { if (!(D0&(1ULL))) {
++err; if (err>cut) return; ++err; if (err>cut) return;
} }
// if(((ez->path.n+5)>(ez->nword*tn*5))||((ez->path.n+5)>(ez->path.m))) {
// fprintf(stderr, "[M::%s::] pn::%d, tn::%d\n", __func__, pn, tn);
// }
ez->path.a[ez->path.n++] = D0;//diff ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff ez->path.a[ez->path.n++] = VN;//diff
inter.cpp
+12 -9
View File
@@ -5776,7 +5776,8 @@ void filter_topN(overlap_region_alloc* ol, kv_ul_ov_t *aln, uint64_t ql, uint64_
uint64_t get_win_info(overlap_region *z, uint64_t wid, int64_t *ys, int64_t *ye, int64_t *err) uint64_t get_win_info(overlap_region *z, uint64_t wid, int64_t *ys, int64_t *ye, int64_t *err)
{ {
if((wid > 0) && (z->w_list.a[wid].y_end != -1) && (z->w_list.a[wid-1].y_end != -1)) { (*err) = -2;
if((wid > 0) && (z->w_list.a[wid].y_end != -1) && (z->w_list.a[wid-1].y_end != -1) && (z->w_list.a[wid].y_end > z->w_list.a[wid-1].y_end)) {
(*ys) = z->w_list.a[wid-1].y_end+1; (*ys) = z->w_list.a[wid-1].y_end+1;
(*ye) = z->w_list.a[wid].y_end; (*ye) = z->w_list.a[wid].y_end;
(*err) = z->w_list.a[wid].error; (*err) = z->w_list.a[wid].error;
@@ -5872,10 +5873,10 @@ uint64_t *buf, uint64_t dp, char *str0, char *str1, kv_ul_ov_t *aln)///[s, e)
} }
void update_shared_intervals(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t *uopt, void update_shared_intervals(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t *uopt,
All_reads *rref, UC_Read* tu, kvec_t_u64_warp* idx, st_mt_t *sps, int64_t ql, int64_t wl, kv_ul_ov_t *aln) All_reads *rref, UC_Read* tu, kvec_t_u64_warp* idx, st_mt_t *sps, int64_t ql, int64_t wl, kv_ul_ov_t *aln, uint64_t rid)
{ {
if(!aln->n) return; if(!aln->n) return;
uint64_t i, k, j, own, srt_n; int64_t dp, old_dp, beg, end; overlap_region *z; uint64_t i, k, own, srt_n; int64_t dp, old_dp, beg, end; overlap_region *z;
for (i = 0; i < ol->length; i++) { for (i = 0; i < ol->length; i++) {
z = &(ol->list[i]); append_unmatched_wins(z, wl); z = &(ol->list[i]); append_unmatched_wins(z, wl);
own = z->w_list.n; z->align_length = (uint32_t)-1; own = z->w_list.n; z->align_length = (uint32_t)-1;
@@ -5904,8 +5905,10 @@ All_reads *rref, UC_Read* tu, kvec_t_u64_warp* idx, st_mt_t *sps, int64_t ql, in
kv_push(uint64_t, idx->a, ((uint32_t)idx->a.a[i])); kv_push(uint64_t, idx->a, ((uint32_t)idx->a.a[i]));
} }
///[beg, end) ///[beg, end)
// fprintf(stderr, "[M::%s::input] beg::%ld, end::%ld, old_dp::%ld, dp::%ld, aln->n::%lu, aln_n::%lu\n", // if(rid == 92) {
// __func__, beg, end, old_dp, dp, (uint64_t)aln->n, aln_n); // fprintf(stderr, "[M::%s::input] beg::%ld, end::%ld, old_dp::%ld, dp::%ld\n",
// __func__, beg, end, old_dp, dp);
// }
if((end > beg) && (end - beg > wl) && (old_dp >= 2) ) { if((end > beg) && (end - beg > wl) && (old_dp >= 2) ) {
idx->a.n = srt_n + idx->a.n = srt_n +
gen_commen_win(rref, uref, ol, idx->a.a+srt_n, idx->a.n-srt_n, beg, end, ql, wl, sps->a, old_dp, tu->seq, tu->seq+wl, aln); gen_commen_win(rref, uref, ol, idx->a.a+srt_n, idx->a.n-srt_n, beg, end, ql, wl, sps->a, old_dp, tu->seq, tu->seq+wl, aln);
@@ -6068,7 +6071,7 @@ static void worker_for_ul_rescall_alignment(void *data, long i, int tid) // call
// if(s->id+i!=41927 && s->id+i!=47072 && s->id+i!=67641 && s->id+i!=90305 && s->id+i!=698342 && s->id+i!=329421) { // if(s->id+i!=41927 && s->id+i!=47072 && s->id+i!=67641 && s->id+i!=90305 && s->id+i!=698342 && s->id+i!=329421) {
// return; // return;
// } // }
// if((s->id+i!=49) /**&& (s->id+i!=44) && (s->id+i!=948)**/) return; // if((s->id+i!=2936) /**&& (s->id+i!=44) && (s->id+i!=948)**/) return;
// fprintf(stderr, "\n[M::%s] rid::%ld, len::%lu, name::%.*s\n", __func__, s->id+i, s->len[i], // fprintf(stderr, "\n[M::%s] rid::%ld, len::%lu, name::%.*s\n", __func__, s->id+i, s->len[i],
// (int32_t)UL_INF.nid.a[s->id+i].n, UL_INF.nid.a[s->id+i].a); // (int32_t)UL_INF.nid.a[s->id+i].n, UL_INF.nid.a[s->id+i].a);
@@ -6098,11 +6101,11 @@ static void worker_for_ul_rescall_alignment(void *data, long i, int tid) // call
gl_chain_flter(&b->olist, &b->correct, &(s->sps[tid]), bl, s->uu, s->opt->diff_ec_ul, winLen, s->len[i], s->uopt, &phase); gl_chain_flter(&b->olist, &b->correct, &(s->sps[tid]), bl, s->uu, s->opt->diff_ec_ul, winLen, s->len[i], s->uopt, &phase);
if(phase) { if(phase) {
fprintf(stderr, "\n[M::%s] rid::%ld, len::%lu, name::%.*s\n", __func__, s->id+i, s->len[i], // fprintf(stderr, "\n[M::%s] rid::%ld, len::%lu, name::%.*s\n", __func__, s->id+i, s->len[i],
(int32_t)UL_INF.nid.a[s->id+i].n, UL_INF.nid.a[s->id+i].a); // (int32_t)UL_INF.nid.a[s->id+i].n, UL_INF.nid.a[s->id+i].a);
if(gen_shared_intervals(&b->olist, s->uu, s->uopt, winLen, &b->r_buf, &(bl->lo))) { if(gen_shared_intervals(&b->olist, s->uu, s->uopt, winLen, &b->r_buf, &(bl->lo))) {
filter_topN(&b->olist, &(bl->lo), s->len[i], winLen, UL_TOPN, bl); filter_topN(&b->olist, &(bl->lo), s->len[i], winLen, UL_TOPN, bl);
update_shared_intervals(&b->olist, s->uu, s->uopt, NULL, &b->ovlp_read, &b->r_buf, &(s->sps[tid]), s->len[i], winLen, &(bl->lo)); update_shared_intervals(&b->olist, s->uu, s->uopt, NULL, &b->ovlp_read, &b->r_buf, &(s->sps[tid]), s->len[i], winLen, &(bl->lo), s->id+i);
ul_lalign(&b->olist, &b->clist, s->uu, s->seq[i], s->len[i], &b->self_read, &b->ovlp_read, ul_lalign(&b->olist, &b->clist, s->uu, s->seq[i], s->len[i], &b->self_read, &b->ovlp_read,
&b->correct, &b->exz, &b->hap, &b->r_buf, s->opt->diff_ec_ul, winLen, &(bl->lo), s->id+i, NULL); &b->correct, &b->exz, &b->hap, &b->r_buf, s->opt->diff_ec_ul, winLen, &(bl->lo), s->id+i, NULL);
// ul_lalign_old_ed(&b->olist, &b->clist, s->uu, s->seq[i], s->len[i], &b->self_read, &b->ovlp_read, // ul_lalign_old_ed(&b->olist, &b->clist, s->uu, s->seq[i], s->len[i], &b->self_read, &b->ovlp_read,