mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-27 12:18:11 +08:00
better uovlp saving
This commit is contained in:
chhylp123
@@ -113,7 +113,7 @@ typedef struct {
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int min_gc_cnt, min_gc_score, sub_diff, best_n;
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float chn_pen_gap, mask_level, pri_ratio;
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///base-alignment
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double bw_thres, diff_ec_ul; int max_n_chain;
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double bw_thres, diff_ec_ul, diff_ec_ul_low; int max_n_chain, ec_ul_round;
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} mg_idxopt_t;
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typedef struct {
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@@ -404,7 +404,8 @@ void hc_gdpchain_destroy(gdpchain_t *b)
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kv_destroy(b->path); kv_destroy(b->v); kv_destroy(b->f); kv_destroy(b->dst_done);
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}
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void init_mg_opt(mg_idxopt_t *opt, int is_HPC, int k, int w, int hap_n, int max_n_chain, double bw_thres, double diff_ec_ul)
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void init_mg_opt(mg_idxopt_t *opt, int is_HPC, int k, int w, int hap_n, int max_n_chain, double bw_thres,
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double diff_ec_ul, double diff_ec_ul_low, int ec_ul_round)
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{
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opt->k = k;
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opt->w = w;
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@@ -432,6 +433,8 @@ void init_mg_opt(mg_idxopt_t *opt, int is_HPC, int k, int w, int hap_n, int max_
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opt->max_n_chain = max_n_chain;
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opt->bw_thres = bw_thres;
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opt->diff_ec_ul = diff_ec_ul;
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opt->diff_ec_ul_low = diff_ec_ul_low;
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opt->ec_ul_round = ec_ul_round;
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}
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void uidx_l_build(ma_ug_t *ug, mg_idxopt_t *opt, int cutoff)
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@@ -2331,10 +2334,59 @@ void replace_ul(overlap_region_alloc* olist, Correct_dumy* dumy, haplotype_evdie
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}
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**/
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uint64_t gl_chain_gen(overlap_region_alloc* olist, const ul_idx_t *uref, kv_ul_ov_t *res, uint32_t rec_trans, void *km)
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uint64_t update_ava_het_site(haplotype_evdience_alloc *h, uint64_t oid, uint64_t *beg, uint64_t *end, uint64_t is_srt)
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{
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uint64_t k, o2 = 0; ul_ov_t *p = NULL;
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uint64_t k, l, i, occ = 0, n = h->length, need_srt = 0; SnpStats *s = NULL;
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haplotype_evdience tt;
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l = beg? (*beg):0; if(end) (*end) = n; if(beg) (*beg) = n;
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if(l < n && h->list[l].overlapID > oid){
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if(end) (*end) = l;
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return 0;
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}
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for (k = l + 1; k <= n; ++k) {
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if(h->list[l].overlapID > oid) {
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if(end) (*end) = l;
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break;
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}
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if (k == n || h->list[k].overlapID != h->list[l].overlapID) {
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if(h->list[l].overlapID == oid) {
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for (i = l; i < k; i++) {
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if(h->list[i].type!=1) continue;
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s = &(h->snp_stat.a[h->list[i].overlapSite]);
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if(s->score == 1 && (!(s->occ_0 < 2 || s->occ_1 < 2))) {
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if(l+occ != i) {
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tt = h->list[l+occ];
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h->list[l+occ] = h->list[i];
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h->list[i] = tt;
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}
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if((occ>0) && (h->list[l+occ].cov<h->list[l+occ-1].cov)) need_srt = 1;
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occ++;
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}
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}
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if(beg) (*beg) = l;
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if(end) (*end) = k;
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break;
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}
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l = k;
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}
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}
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// if(oid == 160) {
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// fprintf(stderr, "###[M::%s] l:%lu, occ:%lu\n", __func__, l, occ);
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// for (k = l; k < l + occ; k++) {
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// fprintf(stderr, "h->list[%lu]:%u\n", k, h->list[k].cov);
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// }
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// }
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if(occ && is_srt && need_srt) {
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radix_sort_hap_ev_cov_srt(h->list+l, h->list+l+occ);
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}
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return occ;
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}
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uint64_t gl_chain_gen(overlap_region_alloc* olist, const ul_idx_t *uref, kv_ul_ov_t *res, uint32_t rec_trans, haplotype_evdience_alloc *hap, void *km)
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{
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uint64_t k, o2 = 0, si = 0, ei = 0; ul_ov_t *p = NULL;
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res->n = 0;
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for (k = 0; k < olist->length; k++) {
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if(olist->list[k].is_match==2) o2++;
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@@ -2351,6 +2403,11 @@ uint64_t gl_chain_gen(overlap_region_alloc* olist, const ul_idx_t *uref, kv_ul_o
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p->ts = olist->list[k].y_pos_s;
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p->te = olist->list[k].y_pos_e+1;
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}
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if(olist->list[k].is_match==2) {
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p->sec = update_ava_het_site(hap, k, &si, &ei, 1);
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assert(p->sec > 0);
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si = ei;
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}
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}
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return o2;
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}
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@@ -2505,54 +2562,6 @@ uint64_t get_het_site(haplotype_evdience_alloc *hap, uint32_t oid)
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return (occ&((uint64_t)0x3FFFFFFF));
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}
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uint64_t update_ava_het_site(haplotype_evdience_alloc *h, uint64_t oid, uint64_t *beg, uint64_t *end, uint64_t is_srt)
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{
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uint64_t k, l, i, occ = 0, n = h->length, need_srt = 0; SnpStats *s = NULL;
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haplotype_evdience tt;
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l = beg? (*beg):0; if(end) (*end) = n; if(beg) (*beg) = n;
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if(l < n && h->list[l].overlapID > oid){
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if(end) (*end) = l;
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return 0;
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}
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for (k = l + 1; k <= n; ++k) {
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if(h->list[l].overlapID > oid) {
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if(end) (*end) = l;
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break;
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}
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if (k == n || h->list[k].overlapID != h->list[l].overlapID) {
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if(h->list[l].overlapID == oid) {
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for (i = l; i < k; i++) {
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if(h->list[i].type!=1) continue;
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s = &(h->snp_stat.a[h->list[i].overlapSite]);
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if(s->score == 1 && (!(s->occ_0 < 2 || s->occ_1 < 2))) {
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if(l+occ != i) {
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tt = h->list[l+occ];
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h->list[l+occ] = h->list[i];
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h->list[i] = tt;
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}
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if((occ>0) && (h->list[l+occ].cov<h->list[l+occ-1].cov)) need_srt = 1;
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occ++;
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}
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}
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if(beg) (*beg) = l;
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if(end) (*end) = k;
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break;
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}
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l = k;
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}
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}
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// if(oid == 160) {
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// fprintf(stderr, "###[M::%s] l:%lu, occ:%lu\n", __func__, l, occ);
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// for (k = l; k < l + occ; k++) {
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// fprintf(stderr, "h->list[%lu]:%u\n", k, h->list[k].cov);
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// }
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// }
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if(occ && is_srt && need_srt) {
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radix_sort_hap_ev_cov_srt(h->list+l, h->list+l+occ);
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}
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return occ;
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}
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int64_t get_chain_x(overlap_region* ot, int64_t q)
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{
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@@ -2724,6 +2733,50 @@ int64_t debug_utg_ct_t(const ul_idx_t *uref, overlap_region* o, utg_ct_t *ct_a,
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return m;
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}
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int64_t get_het_occ(haplotype_evdience *he_a, int64_t he_n, int64_t c_k, int64_t ylen, utg_ct_t *p, int64_t rev)
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{
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int64_t k, occ = 0, ss;
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if(!rev) {
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for (k = c_k; k >= 0; k--) {
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if(he_a[k].cov >= p->s && he_a[k].cov < p->e) {
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occ++;
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} else {
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break;
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}
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}
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for (k = c_k+1; k < he_n; k++) {
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if(he_a[k].cov >= p->s && he_a[k].cov < p->e) {
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occ++;
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} else {
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break;
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}
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}
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} else {
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for (k = c_k; k >= 0; k--) {
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ss = ylen - he_a[k].cov - 1;
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if(ss >= p->s && ss < p->e) {
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occ++;
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} else {
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break;
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}
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}
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for (k = c_k+1; k < he_n; k++) {
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ss = ylen - he_a[k].cov - 1;
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if(ss >= p->s && ss < p->e) {
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occ++;
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} else {
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break;
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}
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}
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}
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assert(occ);
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return occ;
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}
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int64_t rescue_contain_ul_chains(const ul_idx_t *uref, overlap_region* o, haplotype_evdience *he_a, int64_t he_n, utg_ct_t *ct_a, int64_t ct_n,
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kv_ul_ov_t *chains, double diff_ec_ul, int64_t winLen, int64_t rescue_trans, void *km)
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{
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@@ -2761,6 +2814,7 @@ kv_ul_ov_t *chains, double diff_ec_ul, int64_t winLen, int64_t rescue_trans, voi
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} else if(rescue_trans) {
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if(gen_contain_chain(uref, p, o, chains, diff_ec_ul, winLen, km)){
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t0++; chains->a[chains->n-1].el = 0;
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chains->a[chains->n-1].sec = get_het_occ(he_a, he_n, k, uref->ug->u.a[o->y_id].len, p, o->y_pos_strand);
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}
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}
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// if(!ff) t0++;
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@@ -2791,6 +2845,7 @@ kv_ul_ov_t *chains, double diff_ec_ul, int64_t winLen, int64_t rescue_trans, voi
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} else if(rescue_trans) {
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if(gen_contain_chain(uref, p, o, chains, diff_ec_ul, winLen, km)){
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t0++; chains->a[chains->n-1].el = 0;
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chains->a[chains->n-1].sec = get_het_occ(he_a, he_n, k, uref->ug->u.a[o->y_id].len, p, o->y_pos_strand);
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}
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}
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// if(!ff) t0++;
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@@ -2801,6 +2856,7 @@ kv_ul_ov_t *chains, double diff_ec_ul, int64_t winLen, int64_t rescue_trans, voi
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return t0;
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}
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int64_t rescue_trans_ul_chains(const ul_idx_t *uref, overlap_region* o, haplotype_evdience *he_a, int64_t he_n, ma_utg_t *u,
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kv_ul_ov_t *chains, double diff_ec_ul, int64_t winLen, int64_t rescue_trans, uint64_t *cis_occ, void *km)
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{
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@@ -2833,6 +2889,7 @@ kv_ul_ov_t *chains, double diff_ec_ul, int64_t winLen, int64_t rescue_trans, uin
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} else if(rescue_trans) {
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if(gen_contain_chain(uref, &p, o, chains, diff_ec_ul, winLen, km)){
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t0++; chains->a[chains->n-1].el = 0; if(cis_occ) (*cis_occ)++;
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chains->a[chains->n-1].sec = get_het_occ(he_a, he_n, k, uref->ug->u.a[o->y_id].len, &p, o->y_pos_strand);
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}
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}
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// if(!ff) t0++;
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@@ -2863,6 +2920,7 @@ kv_ul_ov_t *chains, double diff_ec_ul, int64_t winLen, int64_t rescue_trans, uin
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} else if(rescue_trans) {
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if(gen_contain_chain(uref, &p, o, chains, diff_ec_ul, winLen, km)){
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t0++; chains->a[chains->n-1].el = 0; if(cis_occ) (*cis_occ)++;
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chains->a[chains->n-1].sec = get_het_occ(he_a, he_n, k, uref->ug->u.a[o->y_id].len, &p, o->y_pos_strand);
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}
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}
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// if(!ff) t0++;
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@@ -3182,7 +3240,7 @@ int64_t gl_chain_refine(overlap_region_alloc* olist, Correct_dumy* dumy, haploty
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ll->tk.n = ll->lo.n = 0;
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kv_ul_ov_t *idx = &(ll->lo);
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ul_contain *ct = uref->ct;
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gl_chain_gen(olist, uref, idx, 0, km);
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gl_chain_gen(olist, uref, idx, 0, hap, km);
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if(idx->n == 0) return 0;
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kv_resize_km(km, ul_ov_t, ll->tk, idx->n);
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kv_resize_km(km, uint64_t, ll->srt.a, idx->n);
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@@ -3687,7 +3745,7 @@ uint64_t mode, All_reads *ridx, ma_ug_t *ug, int64_t debug_i, void *km)
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if (x > qlen+1) x = qlen+1;
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x = find_ul_ov_max(i, res->a, x+G_CHAIN_INDEL);
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if(li->el) csc = mode?retrieve_r_cov_region(uref, li->tn, 0, li->ts, li->te, NULL):retrieve_u_cov_region(uref, li->tn, 0, li->ts, li->te, NULL);
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else csc = trans_sc; //trans overlaps
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else csc = (trans_sc*li->sec); //trans overlaps
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mm_sc = csc; mm_idx = -1;
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// if(i == 37 || i == 36 || i == 35 || i == 32) fprintf(stderr, "*i:%ld, x:%ld, mm_sc:%ld\n", i, x, mm_sc);
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for (j = x; j >= 0; --j) { // collect potential destination vertices
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@@ -3780,10 +3838,11 @@ uint64_t mode, All_reads *ridx, ma_ug_t *ug, int64_t debug_i, void *km)
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if(res->a[k].qs > ex[n_v0+i].qs) res->a[k].qs = ex[n_v0+i].qs;
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if(res->a[k].qs > ex[n_v-i-1].qs) res->a[k].qs = ex[n_v-i-1].qs;
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n_el -= ex[n_v0+i].el; n_el -= ex[n_v-i-1].el;
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ex[n_v0+i].sec = ex[n_v-i-1].sec = SEC_MODE;
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}
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if(((uint32_t)idx[k])&1) {
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if(res->a[k].qs > ex[n_v0+i].qs) res->a[k].qs = ex[n_v0+i].qs;
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n_el -= ex[n_v0+i].el;
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n_el -= ex[n_v0+i].el; ex[n_v0+i].sec = SEC_MODE;
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}
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assert(ex[n_v0].el && ex[n_v-1].el);
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// fprintf(stderr, "[M::%s] k:%ld, qs:%u, qe:%u, chain_occ:%u, chain_score:%u\n", __func__, k,
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@@ -4073,13 +4132,13 @@ void dump_all_chain(kv_ul_ov_t *idx, kv_ul_ov_t *ax, int64_t ax_new_occ, int64_t
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}
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}
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void dump_all_chain_simple(kv_ul_ov_t *idx, kv_ul_ov_t *ax, int64_t ax_new_occ, int64_t qlen,
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int64_t dump_all_chain_simple(kv_ul_ov_t *idx, kv_ul_ov_t *ax, int64_t ax_new_occ, int64_t qlen,
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float primary_cov_rate, float fragement_cov_rate, float primary_fragment_cov_rate,
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float primary_fragment_second_score_rate, float trans_thres)
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{
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if(idx->n <= 0) return;
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if(idx->n <= 0) return 0;
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ul_ov_t *m = &(idx->a[idx->n-1]); //largest chain
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ul_ov_t *a = ax->a + ax->n; int64_t k, z, l, idx_n = idx->n, ovlp, om, ok;
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ul_ov_t *a = ax->a + ax->n; int64_t k, z, l, idx_n = idx->n, ovlp, om, ok, ff = 0;
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// fprintf(stderr, "[M::%s] m->score:%u, m->qs:%u, m->qe:%u, chain_n:%u\n", __func__, m->qn, m->qs, m->qe, m->te-m->ts);
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if(((m->qe-m->qs) > (qlen*primary_cov_rate)) &&
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(check_trans_rate(a+m->ts, m->te-m->ts, trans_thres))) { ///found a primary chain
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@@ -4087,7 +4146,7 @@ float primary_fragment_second_score_rate, float trans_thres)
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a[l] = a[k]; a[l].tn |= ((uint32_t)(0x80000000)); a[l].el = 1;
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l++;
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}
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ax->n += l;
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ax->n += l; ff = 1;
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} else {
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if(((m->qe-m->qs) > (qlen*primary_fragment_cov_rate)) &&
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(check_trans_rate(a+m->ts, m->te-m->ts, trans_thres))) {
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@@ -4098,13 +4157,15 @@ float primary_fragment_second_score_rate, float trans_thres)
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if(ovlp == 0) continue;
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ok = idx->a[k].qe - idx->a[k].qs;
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if(ok > om ) ok = om;
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if((ovlp > ok*0.25) && idx->a[k].qn > (m->qn*primary_fragment_second_score_rate)) break;
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if((ovlp > ok*0.1/**0.25**/) && idx->a[k].qn > (m->qn*primary_fragment_second_score_rate)) break;
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}
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if(k >= idx_n-1) {
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for (k = m->ts; k < m->te; k++) {
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if(a[k].el) a[k].tn |= ((uint32_t)(0x80000000));
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// if(a[k].el) a[k].tn |= ((uint32_t)(0x80000000));
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a[k].tn |= ((uint32_t)(0x80000000));
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}
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ff = 1;
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}
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}
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@@ -4120,8 +4181,10 @@ float primary_fragment_second_score_rate, float trans_thres)
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for (k = 0; k < idx_n; k++) {
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if((idx->a[k].qe - idx->a[k].qs) <= (qlen*fragement_cov_rate)) continue;
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for (z = idx->a[k].ts; z < idx->a[k].te; z++) {
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if(a[z].el) a[z].tn |= ((uint32_t)(0x80000000));
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// if(a[z].el) a[z].tn |= ((uint32_t)(0x80000000));
|
||||
a[z].tn |= ((uint32_t)(0x80000000));
|
||||
}
|
||||
ff = 1;
|
||||
}
|
||||
}
|
||||
/**
|
||||
@@ -4133,6 +4196,13 @@ float primary_fragment_second_score_rate, float trans_thres)
|
||||
radix_sort_ul_ov_srt_qe(a, a + l);
|
||||
ax->n += l;
|
||||
**/
|
||||
for (k = 0, l = 0; k < ax_new_occ; k++) {
|
||||
if(a[k].el || (a[k].tn&((uint32_t)(0x80000000)))) {
|
||||
a[l] = a[k]; l++;
|
||||
}
|
||||
}
|
||||
ax_new_occ = l;
|
||||
|
||||
radix_sort_ul_ov_srt_qe(a, a + ax_new_occ);
|
||||
for (k = 1, l = 0; k <= ax_new_occ; k++) {
|
||||
if (k == ax_new_occ || a[k].qe != a[l].qe) {
|
||||
@@ -4142,6 +4212,7 @@ float primary_fragment_second_score_rate, float trans_thres)
|
||||
}
|
||||
ax->n += ax_new_occ;
|
||||
}
|
||||
return ff;
|
||||
}
|
||||
|
||||
void save_tmp_chains(ul_ov_t *idx_a, uint64_t idx_n, uint64_t *idx_buf_0, uint64_t *idx_buf_1, ul_ov_t *cc_a, uint64_t cc_n, uint64_t *cc_buf)
|
||||
@@ -4158,13 +4229,103 @@ void debug_reverse_chain(ul_ov_t *a, int64_t a_n)
|
||||
}
|
||||
}
|
||||
|
||||
uint32_t quick_primary_assgin(const ul_idx_t *uref, const ug_opt_t *uopt, int64_t bw, double diff_ec_ul, ul_ov_t *a, int64_t a_n)
|
||||
{
|
||||
int64_t k, qo, share, f = 1; ul_ov_t *li, *lk; uint32_t li_v, lk_v;
|
||||
for (k = a_n - 1, li = NULL; k >= 0; k--) {
|
||||
lk = &(a[k]); lk_v = (lk->tn<<1)|lk->rev; lk->sec = SEC_MODE;
|
||||
if(!(lk->tn&((uint32_t)(0x80000000)))) continue;
|
||||
if(li && lk->qe > li->qs) { ///lk is overlapped with li
|
||||
li->tn <<= 1; li->tn >>= 1; lk->tn <<= 1; lk->tn >>= 1;
|
||||
qo = infer_rovlp(li, lk, NULL, NULL, NULL, NULL);
|
||||
li->tn |= ((uint32_t)(0x80000000)); lk->tn |= ((uint32_t)(0x80000000));
|
||||
if(qo && li_v != lk_v && get_ecov_adv(uref, uopt, li_v^1, lk_v^1, bw, diff_ec_ul, qo, 1, &share)) {
|
||||
li->sec = k; f++; ///the end of a chain is a cis overlap
|
||||
} else {
|
||||
f = 0;
|
||||
break;
|
||||
}
|
||||
}
|
||||
li = lk; li_v = lk_v;
|
||||
}
|
||||
return f;
|
||||
}
|
||||
|
||||
void assgin_primary_chains(ul_ov_t *a, int64_t a_n, int64_t is_srt, const ul_idx_t *uref, const ug_opt_t *uopt,
|
||||
uint64_t *track, uint64_t *srt, int64_t bw, double diff_ec_ul, int64_t qlen, int64_t is_ungap)
|
||||
{
|
||||
if(a_n == 0) return;
|
||||
int64_t i, j, k, mm_ovlp, x, csc, mm_sc, mm_idx, qo, share, sc;
|
||||
uint32_t li_v, lj_v; ul_ov_t *li = NULL, *lj = NULL;
|
||||
if(is_srt) {
|
||||
radix_sort_ul_ov_srt_qe(a, a + a_n);
|
||||
for (i = 1, j = 0; i <= a_n; i++) {
|
||||
if (i == a_n || a[i].qe != a[j].qe) {
|
||||
if(i - j > 1) {
|
||||
radix_sort_ul_ov_srt_qs(a+j, a+i);
|
||||
}
|
||||
j = i;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if(uref && uopt && track && srt) {
|
||||
if(quick_primary_assgin(uref, uopt, bw, diff_ec_ul, a, a_n) == 0) {
|
||||
for (i = 0; i < a_n; ++i) {
|
||||
li = &(a[i]); li_v = (li->tn<<1)|li->rev; li->sec = SEC_MODE;
|
||||
mm_sc = csc = 1; mm_idx = -1;
|
||||
if(li->tn&((uint32_t)(0x80000000))) {
|
||||
mm_ovlp = max_ovlp_src(uopt, li_v^1);
|
||||
x = (li->qs + mm_ovlp)*diff_ec_ul;
|
||||
if(x < bw) x = bw;
|
||||
x += li->qs + mm_ovlp;
|
||||
if (x > qlen+1) x = qlen+1;
|
||||
x = find_ul_ov_max(i, a, x+G_CHAIN_INDEL);
|
||||
|
||||
for (j = x; j >= 0; --j) {
|
||||
lj = &(a[j]); lj_v = (lj->tn<<1)|lj->rev;
|
||||
if(lj->qe+G_CHAIN_INDEL <= li->qs) break;//even this pair has a overlap, its length will be very small; just ignore
|
||||
if(is_ungap && (lj->qs >= li->qs+G_CHAIN_INDEL)) continue; // lj is contained in li on the query coordinate; 128 for indel offset
|
||||
if(!(lj->tn&((uint32_t)(0x80000000)))) continue;
|
||||
li->tn <<= 1; li->tn >>= 1; lj->tn <<= 1; lj->tn >>= 1;
|
||||
qo = infer_rovlp(li, lj, NULL, NULL, NULL, NULL);
|
||||
li->tn |= ((uint32_t)(0x80000000)); lj->tn |= ((uint32_t)(0x80000000));
|
||||
if(qo && li_v != lj_v && get_ecov_adv(uref, uopt, li_v^1, lj_v^1, bw, diff_ec_ul, qo, 1, &share)) {
|
||||
sc = csc + pop_sc(track[j]);
|
||||
if(sc > mm_sc) mm_sc = sc, mm_idx = j;
|
||||
}
|
||||
}
|
||||
}
|
||||
track[i] = push_sc_pre(mm_sc, mm_idx);
|
||||
srt[i] = track[i]>>32; srt[i] <<= 32; srt[i] |= i;
|
||||
// fprintf(stderr, "[M::] i->%ld; mm_idx->%ld\n", i, mm_idx);
|
||||
}
|
||||
|
||||
radix_sort_gfa64(srt, srt+a_n);
|
||||
for (k = a_n-1; k >= 0; --k) {
|
||||
i = (uint32_t)srt[k];
|
||||
// if(i < 0 || i >= a_n) fprintf(stderr, "sbsbsbsbsbsb, k->%ld, i->%ld, a_n->%ld\n", k, i, a_n);
|
||||
if(a[i].el && (a[i].tn&((uint32_t)(0x80000000)))) {
|
||||
for (; i >= 0 && (track[i]&((uint64_t)0x80000000)) == 0;) {
|
||||
track[i] |= ((uint64_t)0x80000000); j = i;
|
||||
i = pop_pre(track[i]);
|
||||
if(i >= 0) {
|
||||
a[j].sec = i;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
int64_t gl_chain_refine_advance(overlap_region_alloc* olist, Correct_dumy* dumy, haplotype_evdience_alloc *hap, glchain_t *ll, const ul_idx_t *uref, double diff_ec_ul, int64_t winLen, int64_t qlen, const ug_opt_t *uopt,
|
||||
int64_t debug_i, void *km)
|
||||
{
|
||||
// ll->tk.n = ll->lo.n = 0;
|
||||
kv_ul_ov_t *idx = &(ll->lo);
|
||||
ul_contain *ct = uref->ct;
|
||||
uint64_t o2 = gl_chain_gen(olist, uref, idx, 0, km);
|
||||
uint64_t o2 = gl_chain_gen(olist, uref, idx, 0, hap, km);
|
||||
if(idx->n == 0) return 0;
|
||||
// fprintf(stderr, "[M::%s] qlen:%ld, idx->n:%u\n", __func__, qlen, (uint32_t)idx->n);
|
||||
uint64_t k, an, cn, si = 0, ei = 0, resc = 0, resc_tk = 0, tk_pl = 0, f = 0, occ = 0, cis_occ = 0, t_cis = 0;
|
||||
@@ -4182,7 +4343,7 @@ int64_t debug_i, void *km)
|
||||
olist->list[ll->tk.a[ll->tk.n+k].qn].x_pos_strand = 1;
|
||||
}
|
||||
} else if(o2) {///means there are trans overlaps
|
||||
gl_chain_gen(olist, uref, idx, 1, km);
|
||||
gl_chain_gen(olist, uref, idx, 1, hap, km);
|
||||
kv_resize_km(km, uint64_t, ll->srt.a, idx->n);
|
||||
kv_resize_km(km, uint64_t, hap->snp_srt, idx->n);
|
||||
kv_resize_km(km, ul_ov_t, ll->tk, ll->tk.n+idx->n);
|
||||
@@ -4286,15 +4447,21 @@ int64_t debug_i, void *km)
|
||||
kv_resize_km(km, ul_ov_t, ll->tk, ll->tk.n+idx->n);
|
||||
occ = gl_chain_advance(idx, ll->tk.a+ll->tk.n, uref, uopt, G_CHAIN_BW, diff_ec_ul, qlen, UG_SKIP, dumy->overlapID, ll->srt.a.a, hap->snp_srt.a, G_CHAIN_TRANS_WEIGHT, 1, &R_INF, NULL, debug_i, km);
|
||||
// fprintf(stderr, "***[M::%s] ll->tk.n:%u, occ:%lu\n", __func__, (uint32_t)ll->tk.n, occ);
|
||||
dump_all_chain_simple(idx, &(ll->tk), occ, qlen, P_CHAIN_COV, P_FRAGEMENT_CHAIN_COV,
|
||||
P_FRAGEMENT_PRIMARY_CHAIN_COV, P_FRAGEMENT_PRIMARY_SECOND_COV, G_CHAIN_TRANS_RATE);
|
||||
f = dump_all_chain_simple(idx, &(ll->tk), occ, qlen, P_CHAIN_COV, P_FRAGEMENT_CHAIN_COV,
|
||||
P_FRAGEMENT_PRIMARY_CHAIN_COV, 0.1/**P_FRAGEMENT_PRIMARY_SECOND_COV**/, G_CHAIN_TRANS_RATE);
|
||||
// fprintf(stderr, ">>>[M::%s] ll->tk.n:%u\n", __func__, (uint32_t)ll->tk.n);
|
||||
// dump_all_chain(idx, &(ll->tk), occ, qlen, P_CHAIN_COV, P_CHAIN_SCORE);
|
||||
} else {
|
||||
///for primary chain, each element x: (x->tn & (uint32_t)(0x80000000))
|
||||
radix_sort_ul_ov_srt_qe(ll->tk.a+tk_pl, ll->tk.a+ll->tk.n);
|
||||
assgin_primary_chains(ll->tk.a+tk_pl, ll->tk.n-tk_pl, 1, NULL, NULL, NULL, NULL, G_CHAIN_BW, diff_ec_ul, qlen, 1);
|
||||
// radix_sort_ul_ov_srt_qe(ll->tk.a+tk_pl, ll->tk.a+ll->tk.n);
|
||||
}
|
||||
|
||||
///if f == 0, results have already been sorted by qe|qs
|
||||
if(f) {
|
||||
kv_resize_km(km, uint64_t, ll->srt.a, ll->tk.n-tk_pl); kv_resize_km(km, uint64_t, hap->snp_srt, ll->tk.n-tk_pl);
|
||||
assgin_primary_chains(ll->tk.a+tk_pl, ll->tk.n-tk_pl, 0, uref, uopt, ll->srt.a.a, hap->snp_srt.a, G_CHAIN_BW, diff_ec_ul, qlen, 1);
|
||||
}
|
||||
// debug_reverse_chain(ll->tk.a+tk_pl, ll->tk.n-tk_pl);
|
||||
/**
|
||||
if(idx->n > 0) {
|
||||
@@ -4311,6 +4478,7 @@ uint64_t kv_ul_ov_t_statistics(kv_ul_ov_t *olist, uint64_t qn, int64_t *occ)
|
||||
uint32_t sp = (uint32_t)-1, ep = (uint32_t)-1;
|
||||
for (k = olist->n-1; k >= 0 && olist->a[k].qn == qn; k--) {
|
||||
if(!(olist->a[k].el)) continue;
|
||||
if(!(olist->a[k].tn&((uint32_t)(0x80000000)))) continue;
|
||||
if(sp == (uint32_t)-1 || olist->a[k].qe <= sp) {
|
||||
if(sp != (uint32_t)-1) l += ep - sp;
|
||||
sp = olist->a[k].qs;
|
||||
@@ -4333,7 +4501,7 @@ static void worker_for_ul_scall_alignment(void *data, long i, int tid) // callba
|
||||
uint64_t align = 0;
|
||||
int fully_cov, abnormal;
|
||||
void *km = s->buf?(s->buf[tid]?s->buf[tid]->km:NULL):NULL;
|
||||
// if(s->id+i!=23) return;
|
||||
// if(s->id+i!=927) return;
|
||||
// fprintf(stderr, "[M::%s] rid:%ld\n", __func__, s->id+i);
|
||||
// if (memcmp(UL_INF.nid.a[s->id+i].a, "d0aab024-b3a7-40fb-83cc-22c3d6d951f8", UL_INF.nid.a[s->id+i].n-1)) return;
|
||||
// fprintf(stderr, "[M::%s::] ==> len: %lu\n", __func__, s->len[i]);
|
||||
@@ -4533,13 +4701,15 @@ int alignment_ul_pipeline(uldat_t* sl, const enzyme *fn)
|
||||
return 1;
|
||||
}
|
||||
|
||||
void push_uc_block_t(kv_ul_ov_t *z, char **seq, uint64_t *len, uint64_t b_id)
|
||||
void push_uc_block_t(const ug_opt_t *uopt, kv_ul_ov_t *z, char **seq, uint64_t *len, uint64_t b_id)
|
||||
{
|
||||
uint64_t k, l, rid;
|
||||
for (k = 1, l = 0; k <= z->n; k++) {
|
||||
if(k == z->n || z->a[k].qn != z->a[l].qn) {
|
||||
rid = b_id + z->a[l].qn;
|
||||
append_ul_t(&UL_INF, &rid, NULL, 0, seq[z->a[l].qn], len[z->a[l].qn], z->a + l, k - l, P_CHAIN_COV);
|
||||
// fprintf(stderr, "rid->%lu, b_id->%lu, l->%lu, z->a[l].qn->%u, len[z->a[l].qn]->%lu, seq[z->a[l].qn]->%u\n", rid, b_id, l, z->a[l].qn, len[z->a[l].qn], seq[z->a[l].qn]?1:0);
|
||||
append_ul_t(&UL_INF, &rid, NULL, 0, seq[z->a[l].qn], len[z->a[l].qn], z->a + l, k - l, P_CHAIN_COV, uopt);
|
||||
// append_ul_t_back(&UL_INF, &rid, NULL, 0, seq[z->a[l].qn], len[z->a[l].qn], z->a + l, k - l, P_CHAIN_COV);
|
||||
l = k;
|
||||
}
|
||||
}
|
||||
@@ -4565,11 +4735,12 @@ static void *worker_ul_scall_pipeline(void *data, int step, void *in) // callbac
|
||||
REALLOC(s->seq, s->m);
|
||||
}
|
||||
|
||||
append_ul_t(&UL_INF, NULL, p->ks->name.s, p->ks->name.l, NULL, 0, NULL, 0, P_CHAIN_COV);
|
||||
append_ul_t(&UL_INF, NULL, p->ks->name.s, p->ks->name.l, NULL, 0, NULL, 0, P_CHAIN_COV, s->uopt);
|
||||
l = p->ks->seq.l;
|
||||
MALLOC(s->seq[s->n], l);
|
||||
s->sum_len += l;
|
||||
memcpy(s->seq[s->n], p->ks->seq.s, l);
|
||||
// fprintf(stderr, "s->n->%d, l->%lu\n", s->n, l);
|
||||
s->len[s->n++] = l;
|
||||
if (s->sum_len >= p->chunk_size) break;
|
||||
}
|
||||
@@ -4633,13 +4804,13 @@ static void *worker_ul_scall_pipeline(void *data, int step, void *in) // callbac
|
||||
p->num_corrected_bases += s->num_corrected_bases;
|
||||
p->num_recorrected_bases += s->num_recorrected_bases;
|
||||
for (i = 0; i < p->n_thread; ++i) {
|
||||
push_uc_block_t(&(s->ll[i].tk), s->seq, s->len, s->id);
|
||||
push_uc_block_t(s->uopt, &(s->ll[i].tk), s->seq, s->len, s->id);
|
||||
free(s->ll[i].tk.a);
|
||||
}
|
||||
for (i = 0; i < (uint64_t)s->n; ++i) {
|
||||
rid = s->id + i;
|
||||
if(UL_INF.n > rid && UL_INF.a[rid].rlen != s->len[i]) {
|
||||
append_ul_t(&UL_INF, &rid, NULL, 0, s->seq[i], s->len[i], NULL, 0, P_CHAIN_COV);
|
||||
append_ul_t(&UL_INF, &rid, NULL, 0, s->seq[i], s->len[i], NULL, 0, P_CHAIN_COV, s->uopt);
|
||||
}
|
||||
free(s->seq[i]);
|
||||
}
|
||||
@@ -4701,7 +4872,7 @@ void print_ul_ov_t(ul_ov_t *xs, const char* cmd)
|
||||
"+-"[xs->rev], (int)Get_NAME_LENGTH(R_INF, ((xs->tn<<1)>>1)), Get_NAME(R_INF, ((xs->tn<<1)>>1)), xs->ts, xs->te);
|
||||
}
|
||||
|
||||
void gl_rg2ug_gen(ul_vec_t *r_cl, kv_ul_ov_t *u_cl, const ul_idx_t *uref, uint64_t is_el)
|
||||
void gl_rg2ug_gen(ul_vec_t *r_cl, kv_ul_ov_t *u_cl, const ul_idx_t *uref, uint64_t is_el, uint64_t n_pchain)
|
||||
{
|
||||
uint64_t k, a_k, a_n; uc_block_t *z; utg_rid_dt *a; ul_ov_t *p;
|
||||
u_cl->n = 0;
|
||||
@@ -4709,6 +4880,7 @@ void gl_rg2ug_gen(ul_vec_t *r_cl, kv_ul_ov_t *u_cl, const ul_idx_t *uref, uint64
|
||||
z = &(r_cl->bb.a[k]);
|
||||
if(z->base) continue;
|
||||
if(is_el && (!(z->el))) continue;
|
||||
if(z->pchain == n_pchain) continue;
|
||||
a = get_r_ug_region(uref->r_ug, &a_n, z->hid);
|
||||
if(!a) continue;
|
||||
for (a_k = 0; a_k < a_n; a_k++) {
|
||||
@@ -4719,7 +4891,7 @@ void gl_rg2ug_gen(ul_vec_t *r_cl, kv_ul_ov_t *u_cl, const ul_idx_t *uref, uint64
|
||||
// (int32_t)(a[a_k].u>>1)+1, "lc"[uref->ug->u.a[a[a_k].u>>1].circ], uref->ug->u.a[a[a_k].u>>1].len,
|
||||
// "+-"[a[a_k].u&1], a[a_k].off);
|
||||
rov2uov(z->hid, uref, &(a[a_k]), z, p, 1);
|
||||
p->el = 1; p->tn <<= 1; p->tn |= p->rev; p->qn = uref->r_ug->idx[z->hid] + a_k;//for linear chain
|
||||
p->el = 1; p->tn <<= 1; p->tn |= p->rev; p->qn = k/**uref->r_ug->idx[z->hid] + a_k**/;//for linear chain
|
||||
// fprintf(stderr, "[M::%s::id->%ld] idx->n:%lu\n", __func__, ulid, (uint64_t)idx->n);
|
||||
// fprintf(stderr, "-[M::%s::] %u\t%u\t%c\tutg%.6d%c(%u)\t%u\t%u\n", __func__, p->qs, p->qe, "+-"[p->rev],
|
||||
// (int32_t)(p->tn>>1)+1, "lc"[uref->ug->u.a[p->tn>>1].circ], uref->ug->u.a[p->tn>>1].len, p->ts, p->te);
|
||||
@@ -6356,14 +6528,14 @@ int64_t bw, double diff_ec_ul, int64_t max_skip, int64_t ulid)
|
||||
// if(ulid != 814) return 0;
|
||||
kv_ul_ov_t *idx = &(ll->lo), *init = &(ll->tk); int64_t max_idx;
|
||||
idx->n = init->n = 0;
|
||||
gl_rg2ug_gen(rch, idx, uref, 1);
|
||||
gl_rg2ug_gen(rch, idx, uref, 1, 2);
|
||||
if(idx->n == 0) return 0;
|
||||
///generate linear chains
|
||||
gen_linear_chains(idx, init, uref, uopt, bw, diff_ec_ul, rch->rlen, max_skip, ll, sps);
|
||||
assert(idx->n);
|
||||
if(idx->n == 0) return 0;
|
||||
fprintf(stderr, "\n++[M::%s::%.*s(id:%ld), len:%u] idx->n:%lu\n", __func__, UL_INF.nid.a[ulid].n, UL_INF.nid.a[ulid].a,
|
||||
ulid, rch->rlen, (uint64_t)idx->n);
|
||||
// fprintf(stderr, "\n++[M::%s::%.*s(id:%ld), len:%u] idx->n:%lu\n", __func__, UL_INF.nid.a[ulid].n, UL_INF.nid.a[ulid].a,
|
||||
// ulid, rch->rlen, (uint64_t)idx->n);
|
||||
|
||||
dump_linear_chain(uref->ug->g, idx, init, &(gdp->l), rch->rlen);
|
||||
// fprintf(stderr, "\n+++[M::%s::id->%ld, len->%u] idx->n:%lu\n", __func__, ulid, rch->rlen, (uint64_t)idx->n);
|
||||
@@ -6384,15 +6556,15 @@ int64_t bw, double diff_ec_ul, int64_t max_skip, int64_t ulid)
|
||||
// __ac_X31_hash_string("hehe");
|
||||
|
||||
return 1;
|
||||
} else {
|
||||
uint64_t i;
|
||||
fprintf(stderr, "unsuccess->[M::%s::id->%ld, len->%u] gdp->l.n:%lu\n", __func__, ulid, rch->rlen, (uint64_t)gdp->l.n);
|
||||
for (i = 0; i < gdp->l.n; ++i) {
|
||||
fprintf(stderr, "(%lu)\t%u\t%u\t%c\tutg%.6d%c(%u)\t%u\t%u\tsrc:%u\tscore:%d\n",
|
||||
i, gdp->l.a[i].qs, gdp->l.a[i].qe, "+-"[gdp->l.a[i].v&1], (int32_t)(gdp->l.a[i].v>>1)+1, "lc"[uref->ug->u.a[gdp->l.a[i].v>>1].circ], uref->ug->u.a[gdp->l.a[i].v>>1].len,
|
||||
gdp->l.a[i].rs, gdp->l.a[i].re, gdp->l.a[i].v^1, gdp->l.a[i].score);
|
||||
}
|
||||
}
|
||||
} // else {
|
||||
// uint64_t i;
|
||||
// fprintf(stderr, "unsuccess->[M::%s::id->%ld, len->%u] gdp->l.n:%lu\n", __func__, ulid, rch->rlen, (uint64_t)gdp->l.n);
|
||||
// for (i = 0; i < gdp->l.n; ++i) {
|
||||
// fprintf(stderr, "(%lu)\t%u\t%u\t%c\tutg%.6d%c(%u)\t%u\t%u\tsrc:%u\tscore:%d\n",
|
||||
// i, gdp->l.a[i].qs, gdp->l.a[i].qe, "+-"[gdp->l.a[i].v&1], (int32_t)(gdp->l.a[i].v>>1)+1, "lc"[uref->ug->u.a[gdp->l.a[i].v>>1].circ], uref->ug->u.a[gdp->l.a[i].v>>1].len,
|
||||
// gdp->l.a[i].rs, gdp->l.a[i].re, gdp->l.a[i].v^1, gdp->l.a[i].score);
|
||||
// }
|
||||
// }
|
||||
|
||||
|
||||
|
||||
@@ -6415,8 +6587,8 @@ static void worker_for_ul_gchains_alignment(void *data, long i, int tid)
|
||||
if(p->dd == 1) return; //fully aligned
|
||||
if(p->bb.n == 1 && p->bb.a[0].base) return;///no alignment
|
||||
utepdat_t *s = (utepdat_t*)data;
|
||||
s->sum_len++;
|
||||
s->n += direct_gchain(s->buf[tid], p, &(s->ll[tid]), &(s->gdp[tid]), &(s->sps[tid]), &(s->hab[tid]->hap), s->uu, s->uopt, G_CHAIN_BW, s->opt->diff_ec_ul, UG_SKIP, i);
|
||||
s->hab[tid]->num_read_base++;
|
||||
s->hab[tid]->num_correct_base += direct_gchain(s->buf[tid], p, &(s->ll[tid]), &(s->gdp[tid]), &(s->sps[tid]), &(s->hab[tid]->hap), s->uu, s->uopt, G_CHAIN_BW, s->opt->diff_ec_ul, UG_SKIP, i);
|
||||
// gl_chain_refine_advance(&b->olist, &b->correct, &b->hap, bl, s->uu, s->opt->diff_ec_ul, winLen, s->len[i], s->uopt, s->id+i, km);
|
||||
}
|
||||
|
||||
@@ -6434,6 +6606,7 @@ void work_ul_gchains(uldat_t *sl)
|
||||
kt_for(sl->n_thread, worker_for_ul_gchains_alignment, &s, UL_INF.n);
|
||||
|
||||
for (i = 0; i < sl->n_thread; ++i) {
|
||||
s.sum_len += s.hab[i]->num_read_base; s.n += s.hab[i]->num_correct_base;
|
||||
ha_ovec_destroy(s.hab[i]); mg_tbuf_destroy(s.buf[i]); hc_glchain_destroy(&(s.ll[i]));
|
||||
hc_gdpchain_destroy(&(s.gdp[i])); kv_destroy(s.mzs[i]); kv_destroy(s.sps[i]);
|
||||
}
|
||||
@@ -6674,6 +6847,40 @@ void determine_connective_adv(all_ul_t *m, const ug_opt_t *uopt, int64_t bw, dou
|
||||
}
|
||||
}
|
||||
|
||||
void determine_connective_backtrack(all_ul_t *m, const ug_opt_t *uopt, ul_vec_t *p, uint32_t ii, uint64_t rid)
|
||||
{
|
||||
assert((!p->bb.a[ii].base)&&(p->bb.a[ii].hid == rid)&&(p->bb.a[ii].el));
|
||||
if(ii <= 0) return;
|
||||
if(!(p->bb.a[ii].pchain)) return; ///not a primary chain
|
||||
if(p->bb.a[ii].pidx == (uint32_t)-1) return; ///not connected
|
||||
uint32_t li_v, lk_v, z, qn, tn; int32_t r; uc_block_t *li = NULL, *lk = NULL; asg_arc_t t;
|
||||
li = &(p->bb.a[ii]); li_v = (((uint32_t)(li->hid))<<1)|((uint32_t)(li->rev)); li_v^=1;
|
||||
if((li->te - li->ts) < Get_READ_LENGTH(R_INF, li->hid)) return;
|
||||
ma_hit_t_alloc *x = &(uopt->sources[li_v>>1]);
|
||||
int64_t min_ovlp = uopt->min_ovlp;
|
||||
int64_t max_hang = uopt->max_hang;
|
||||
|
||||
for (lk = &(p->bb.a[li->pidx]); lk; ) {
|
||||
lk_v = (((uint32_t)(lk->hid))<<1)|((uint32_t)(lk->rev)); lk_v^=1;
|
||||
assert((!(lk->base)) && (lk->pchain) && (lk->el) );
|
||||
if((lk->te - lk->ts) >= Get_READ_LENGTH(R_INF, lk->hid)) {
|
||||
for (z = 0; z < x->length; z++) {
|
||||
qn = Get_qn(x->buffer[z]);
|
||||
tn = Get_tn(x->buffer[z]);
|
||||
if(qn == (li_v>>1) && tn == (lk_v>>1)) {
|
||||
r = ma_hit2arc(&(x->buffer[z]), Get_READ_LENGTH(R_INF, li_v>>1), Get_READ_LENGTH(R_INF, lk_v>>1),
|
||||
max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
|
||||
if(r < 0) continue;
|
||||
if((t.ul>>32) != li_v || t.v != lk_v) continue;
|
||||
break;
|
||||
}
|
||||
}
|
||||
if(z < x->length) x->buffer[z].bl++;
|
||||
}
|
||||
lk = ((lk->pidx==(uint32_t)-1)?NULL:&(p->bb.a[lk->pidx]));
|
||||
}
|
||||
}
|
||||
|
||||
static void update_ovlp_src(void *data, long i, int tid) // callback for kt_for()
|
||||
{
|
||||
uldat_t *sl = (uldat_t *)data;
|
||||
@@ -6684,7 +6891,8 @@ static void update_ovlp_src(void *data, long i, int tid) // callback for kt_for(
|
||||
a_n = UL_INF.ridx.idx.a[i+1] - UL_INF.ridx.idx.a[i];
|
||||
for (k = 0; k < a_n; k++) {
|
||||
///note: we only label reliable chains
|
||||
determine_connective_adv(&UL_INF, sl->uopt, G_CHAIN_BW, sl->opt->diff_ec_ul, &(UL_INF.a[a[k]>>32]), (uint32_t)(a[k]), i);
|
||||
determine_connective_backtrack(&UL_INF, sl->uopt, &(UL_INF.a[a[k]>>32]), (uint32_t)(a[k]), i);
|
||||
// determine_connective_adv(&UL_INF, sl->uopt, G_CHAIN_BW, sl->opt->diff_ec_ul, &(UL_INF.a[a[k]>>32]), (uint32_t)(a[k]), i);
|
||||
// determine_connective(&UL_INF, sl->uopt, G_CHAIN_BW, sl->opt->diff_ec_ul,
|
||||
// &(UL_INF.a[a[k]>>32]), (uint32_t)(a[k]), i);
|
||||
}
|
||||
@@ -7226,7 +7434,7 @@ void ul_resolve(ma_ug_t *ug, const asg_t *rg, const ug_opt_t *uopt, int hap_n)
|
||||
{
|
||||
fprintf(stderr, "[M::%s::] ==> UL\n", __func__);
|
||||
mg_idxopt_t opt;
|
||||
init_mg_opt(&opt, 0, 19, 10, hap_n, 0, 0, 0.05);
|
||||
init_mg_opt(&opt, 0, 19, 10, hap_n, 0, 0, 0.05, asm_opt.ul_error_rate_low, asm_opt.ul_ec_round);
|
||||
int exist = (asm_opt.load_index_from_disk? uidx_load(&ha_flt_tab, &ha_idx, asm_opt.output_file_name) : 0);
|
||||
if(exist == 0) uidx_build(ug, &opt);
|
||||
if(exist == 0) uidx_write(ha_flt_tab, ha_idx, asm_opt.output_file_name);
|
||||
@@ -7993,7 +8201,7 @@ void ul_load(const ug_opt_t *uopt)
|
||||
int32_t cutoff;
|
||||
init_aux_table(); ha_opt_update_cov(&asm_opt, asm_opt.hom_cov);
|
||||
cutoff = asm_opt.max_n_chain;
|
||||
init_mg_opt(&opt, !(asm_opt.flag&HA_F_NO_HPC), 19, 10, cutoff, asm_opt.max_n_chain, asm_opt.ul_error_rate, asm_opt.ul_error_rate);
|
||||
init_mg_opt(&opt, !(asm_opt.flag&HA_F_NO_HPC), 19, 10, cutoff, asm_opt.max_n_chain, asm_opt.ul_error_rate, asm_opt.ul_error_rate, asm_opt.ul_error_rate_low, asm_opt.ul_ec_round);
|
||||
init_uldat_t(&sl, NULL, NULL, &opt, 500000000, asm_opt.thread_num, uopt, NULL);
|
||||
|
||||
if(!load_all_ul_t(&UL_INF, asm_opt.output_file_name, &R_INF)) {
|
||||
@@ -8018,7 +8226,7 @@ void ul_refine_alignment(const ug_opt_t *uopt, asg_t *sg)
|
||||
mg_idxopt_t opt; uldat_t sl; int32_t cutoff;
|
||||
init_aux_table(); ha_opt_update_cov(&asm_opt, asm_opt.hom_cov);
|
||||
cutoff = asm_opt.max_n_chain;
|
||||
init_mg_opt(&opt, !(asm_opt.flag&HA_F_NO_HPC), 19, 10, cutoff, asm_opt.max_n_chain, asm_opt.ul_error_rate, asm_opt.ul_error_rate);
|
||||
init_mg_opt(&opt, !(asm_opt.flag&HA_F_NO_HPC), 19, 10, cutoff, asm_opt.max_n_chain, asm_opt.ul_error_rate, asm_opt.ul_error_rate, asm_opt.ul_error_rate_low, asm_opt.ul_ec_round);
|
||||
ul_idx_t *uu = gen_ul_idx_t(uopt, sg, 0, 0);///record contained reads; is_el = is_del = 0
|
||||
init_uldat_t(&sl, NULL, NULL, &opt, 500000000, asm_opt.thread_num, uopt, uu); sl.rg = sg;
|
||||
work_ul_gchains(&sl);
|
||||
|
||||
Reference in New Issue
Block a user