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done second alignment

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chhylp123
2022-10-09 16:59:54 -04:00
parent 2443e63ef5
commit 1d0562ebd1
5 changed files with 421 additions and 30 deletions
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anchor.cpp
+70 -3
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@@ -1112,7 +1112,6 @@ void lchain_qgen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, ui
const ul_idx_t *udb, uint32_t apend_be, overlap_region* tf, uint64_t max_n_chain,
int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check, uint32_t gen_off)
{
// fprintf(stderr, "+[M::%s]\n", __func__);
uint64_t i, k, l, m, sm, cn = cl->length; overlap_region *r; ///srt = 0
clear_overlap_region_alloc(ol);
clear_fake_cigar(&(tf->f_cigar));
@@ -1148,6 +1147,12 @@ void lchain_qgen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, ui
}
}
cl->length = m;
// fprintf(stderr, "+[M::%s] cn::%lu, m::%lu, ol->length::%lu\n", __func__, cn, m, ol->length);
// for (k = 0; k < ol->length; k++) {
// fprintf(stderr, "---[M::%s::utg%.6dl] q[%d, %d), t[%d, %d), khit_off::%u\n", __func__,
// (int32_t)ol->list[k].y_id+1, ol->list[k].x_pos_s, ol->list[k].x_pos_e+1,
// ol->list[k].y_pos_s, ol->list[k].y_pos_e+1, ol->list[k].non_homopolymer_errors);
// }
k = ol->length;
@@ -1183,13 +1188,74 @@ void lchain_qgen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, ui
ks_introsort_or_xs(ol->length, ol->list);
}
void lchain_qgen_mcopy(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb,
const ul_idx_t *udb, uint32_t apend_be, uint64_t max_n_chain, int64_t max_skip, int64_t max_iter,
int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check,
uint32_t gen_off)
{
// fprintf(stderr, "+[M::%s]\n", __func__);
uint64_t i, k, l, m, cn = cl->length, yid; overlap_region *r; ///srt = 0
clear_overlap_region_alloc(ol);
for (l = 0, k = 1, m = 0; k <= cn; k++) {
if((k == cn) || (cl->list[k].readID != cl->list[l].readID)) {
if(cl->list[l].readID != rid) {
yid = cl->list[l].readID;
m += lchain_qdp_mcopy(cl, l, k-l, m, &(cl->chainDP), ol, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate,
rid, rl, rdb?Get_READ_LENGTH((*rdb), yid):udb->ug->u.a[yid].len, quick_check, apend_be, gen_off);
}
l = k;
}
}
cl->length = m;
// for (k = 0; k < ol->length; k++) {
// fprintf(stderr, "---[M::%s::utg%.6dl] q[%d, %d), t[%d, %d), khit_off::%u\n", __func__,
// (int32_t)ol->list[k].y_id+1, ol->list[k].x_pos_s, ol->list[k].x_pos_e+1,
// ol->list[k].y_pos_s, ol->list[k].y_pos_e+1, ol->list[k].non_homopolymer_errors);
// }
k = ol->length;
if (ol->length > max_n_chain) {
int32_t w, n[4], s[4]; overlap_region t;
n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
ks_introsort_or_ss(ol->length, ol->list); ///srt = 1;
for (i = 0; i < ol->length; ++i) {
r = &(ol->list[i]);
w = ha_ov_type(r, rl);
++n[w];
if (((uint64_t)n[w]) == max_n_chain) s[w] = r->shared_seed;
}
if (s[0] > 0 || s[1] > 0 || s[2] > 0 || s[3] > 0) {
// n[0] = n[1] = n[2] = n[3] = 0;
for (i = 0, k = 0; i < ol->length; ++i) {
r = &(ol->list[i]);
w = ha_ov_type(r, rl);
// ++n[w];
// if (((int)n[w] <= max_n_chain) || (r->shared_seed >= s[w] && s[w] >= (asm_opt.k_mer_length<<1))) {
if (r->shared_seed >= s[w]) {
if (k != i) {
t = ol->list[k];
ol->list[k] = ol->list[i];
ol->list[i] = t;
}
++k;
}
}
ol->length = k;
}
}
ks_introsort_or_xs(ol->length, ol->list);
}
void set_lchain_dp_op(uint32_t is_accurate, uint32_t mz_k, int64_t *max_skip, int64_t *max_iter, int64_t *max_dis, double *chn_pen_gap, double *chn_pen_skip, int64_t *quick_check)
{
double div, pen_gap, pen_skip, tmp;
if(is_accurate) {
(*quick_check) = 1; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.01; pen_gap = 0.5f; pen_skip = 0.0005f;
} else {
(*quick_check) = 1; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.1; pen_gap = 0.5f; pen_skip = 0.0005f;
(*quick_check) = 0; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.1; pen_gap = 0.5f; pen_skip = 0.0005f;
}
tmp = expf(-div * (double)mz_k);///0.60049557881 -> HiFi; 0.18268352405 -> ont
*chn_pen_gap = pen_gap * tmp;///0.300247789405 -> HiFi; 0.091341762025 -> ont
@@ -1208,6 +1274,7 @@ void ul_map_lchain(ha_abufl_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t
// minimizers_gen(ab, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, dbg_ct, sp, high_occ, low_occ);
minimizers_qgen(ab, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, NULL, uref, dbg_ct, sp, high_occ, low_occ);
// lchain_gen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
lchain_qgen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
// lchain_qgen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
///no need to sort here, overlap_list has been sorted at lchain_gen
lchain_qgen_mcopy(cl, overlap_list, rid, rl, NULL, uref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
}