mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-30 02:28:12 +08:00
ont overlapping
This commit is contained in:
chhylp123
+28
-2
@@ -1050,6 +1050,21 @@ void ha_ec(int64_t round, int num_pround, int des_idx, uint64_t *tot_b, uint64_t
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}
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int ha_ec_dbg(void)
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{
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int hom_cov, het_cov;
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ha_idx = ha_pt_gen(&asm_opt, 0, 0, 0, &R_INF, &hom_cov, &het_cov); // build the index
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asm_opt.hom_cov = hom_cov; asm_opt.het_cov = het_cov;
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ha_opt_update_cov(&asm_opt, hom_cov);
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cal_ec_r_dbg(asm_opt.thread_num, R_INF.total_reads);
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ha_pt_destroy(ha_idx); ha_idx = NULL;
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return 0;
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}
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void ha_overlap_and_correct(int round)
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{
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int i, hom_cov, het_cov, r_out = 0;
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@@ -2003,8 +2018,7 @@ int ha_assemble_ovec(void)
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ha_flt_tab = ha_idx = NULL;
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// construct hash table for high occurrence k-mers
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if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL)
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{
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if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL) {
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ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0, 0);
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ha_opt_update_cov(&asm_opt, hom_cov);
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}
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@@ -2026,6 +2040,18 @@ int ha_assemble_ovec(void)
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return 0;
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}
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int ha_assemble_ovec_cc(void)
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{
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ha_idx = NULL;
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ha_opt_reset_to_round(&asm_opt, 0); // this update asm_opt.roundID and a few other fields
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ha_ec_dbg();
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// Output_PAF0(R_INF.paf, "0");
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destory_All_reads(&R_INF);
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return 0;
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}
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int ha_assemble(void)
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{
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// debug_mc_g_t(MC_NAME);
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@@ -51,5 +51,6 @@ ha_ovec_buf_t *ha_ovec_buf_init(void *km, int is_final, int save_ov, int is_ug);
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void ha_ovec_destroy(ha_ovec_buf_t *b);
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int64_t ha_ovec_mem(const ha_ovec_buf_t *b, int64_t *mem_a);
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int ha_assemble_ovec(void);
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int ha_ec_dbg(void);
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#endif
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+1
-1
@@ -5,7 +5,7 @@
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#include <pthread.h>
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#include <stdint.h>
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#define HA_VERSION "0.24.0-r702"
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#define HA_VERSION "0.24.0-r703"
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#define VERBOSE 0
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+138
@@ -63,6 +63,23 @@ typedef struct {
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uint8_t *cr;
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} ec_ovec_buf_t;
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typedef struct {
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uint32_t n_thread, n_a, chunk_size, cn;
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FILE *fp;
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} cal_ec_r_dbg_t;
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typedef struct {
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ma_hit_t *a;
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size_t n, m;
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asg16_v ec;
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} r_dbg_step_res_t;
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typedef struct { // data structure for each step in kt_pipeline()
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ec_ovec_buf_t *buf;
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r_dbg_step_res_t *res;
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uint32_t si, ei;
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} cal_ec_r_dbg_step_t;
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ec_ovec_buf_t* gen_ec_ovec_buf_t(uint32_t n);
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void destroy_ec_ovec_buf_t(ec_ovec_buf_t *p);
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@@ -3352,6 +3369,61 @@ static void worker_hap_ec(void *data, long i, int tid)
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**/
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}
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static void worker_hap_ec_dbg_paf(void *data, long i, int tid)
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{
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ec_ovec_buf_t0 *b = &(((cal_ec_r_dbg_step_t*)data)->buf->a[tid]);
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r_dbg_step_res_t *rr = &(((cal_ec_r_dbg_step_t*)data)->res[tid]);
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uint32_t high_occ = asm_opt.hom_cov * (2.0 - HA_KMER_GOOD_RATIO);
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uint32_t low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO;
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overlap_region *aux_o = NULL; i += ((cal_ec_r_dbg_step_t*)data)->si;
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// debug_retrive_bqual(D, &b->v8t, i, 256); return;
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recover_UC_Read(&b->self_read, &R_INF, i);
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h_ec_lchain(b->ab, i, b->self_read.seq, b->self_read.length, asm_opt.mz_win, asm_opt.k_mer_length, &R_INF, &b->olist, &b->clist, ((asm_opt.is_ont)?(0.05):(0.02)), asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 3, 0.7, 2, 32, COV_W);///ONT high error
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aux_o = fetch_aux_ovlp(&b->olist);///must be here
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// stderr_phase_ovlp(&b->olist);
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gen_hc_r_alin_ea(&b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT, 1, &b->v16, &b->v64, &(R_INF.paf[i]), 0);
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uint32_t k, m, tl; overlap_region *z; bit_extz_t ez; ma_hit_t *t;
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for (k = 0; k < b->olist.length; k++) {
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z = &(b->olist.list[k]);
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if(!(z->w_list.n)) continue;
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tl = Get_READ_LENGTH((R_INF), z->y_id);
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for (m = 0; m < z->w_list.n; m++) {
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if(is_ualn_win(z->w_list.a[m])) continue;
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set_bit_extz_t(ez, (*z), m);
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kv_pushp(ma_hit_t, *rr, &t);
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t->qns = z->x_id; t->qns = t->qns << 32;
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t->tn = z->y_id;
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t->qns = t->qns | (uint64_t)(z->w_list.a[m].x_start);
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t->qe = z->w_list.a[m].x_end + 1;
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t->ts = z->w_list.a[m].y_start;
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t->te = z->w_list.a[m].y_end + 1;
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t->rev = z->y_pos_strand;
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t->bl = rr->ec.n;
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kv_resize(uint16_t, rr->ec, rr->ec.n + ez.cigar.n);
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memcpy(rr->ec.a + rr->ec.n, ez.cigar.a, ez.cigar.n * sizeof((*(rr->ec.a))));
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rr->ec.n += ez.cigar.n;
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t->cc = rr->ec.n - t->bl;
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if(t->rev) {
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t->ts = tl - z->w_list.a[m].y_end - 1;
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t->te = tl - z->w_list.a[m].y_start;
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}
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}
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}
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}
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uint32_t adjust_exact_match(asg16_v *in, int64_t xs0, int64_t xe0, int64_t ys0, int64_t ye0, uint64_t *rxs, uint64_t *rxe, uint64_t *rys, uint64_t *rye, uint32_t rev)
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{
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*rxs = *rxe = *rys = *rye = 0;
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@@ -6106,6 +6178,72 @@ void cal_ec_r(uint64_t n_thre, uint64_t round, uint64_t n_round, uint64_t n_a, u
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// }
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}
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void print_ov_dbg_paf(FILE *fp, char *ref_str, char *ref_id, int32_t ref_id_n, char *qry_str, char *qry_id, int32_t qry_id_n, uint64_t rs, uint64_t re, uint64_t rl, uint64_t qs, uint64_t qe, uint64_t ql, uint64_t rev, bit_extz_t *ez, char *ezh)
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{
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uint64_t ci = 0; uint16_t c; uint32_t cl;
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fprintf(fp, "%.*s\t%lu\t%lu\t%lu\t", qry_id_n, qry_id, ql, qs, qe);
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fprintf(fp, "%c\t", "+-"[rev]);
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fprintf(fp, "%.*s\t%lu\t%lu\t%lu\t", ref_id_n, ref_id, rl, rs, re);
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fprintf(fp, "255\tcg:Z:");
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while (ci < ez->cigar.n) {
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ci = pop_trace(&(ez->cigar), ci, &c, &cl);
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fprintf(fp, "%u%c", cl, ezh[c]);
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}
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fprintf(fp, "\n");
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}
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static void *worker_ov_dbg_pipeline(void *data, int step, void *in) // callback for kt_pipeline()
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{
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cal_ec_r_dbg_t *p = (cal_ec_r_dbg_t*)data; char cm[4]; cm[0] = 'M'; cm[1] = 'M'; cm[2] = 'I'; cm[3] = 'D';
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// cal_ec_r_dbg_step_t
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if (step == 0) { // step 1: read a block of sequences
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cal_ec_r_dbg_step_t *s; CALLOC(s, 1);
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s->si = p->cn; p->cn += p->chunk_size;
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if(p->cn > p->n_a) p->cn = p->n_a; s->ei = p->cn;
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if(s->si >= s->ei) free(s);
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else return s;
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} else if (step == 1) { // step 2: alignment
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cal_ec_r_dbg_step_t *s = (cal_ec_r_dbg_step_t*)in;
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s->buf = gen_ec_ovec_buf_t(p->n_thread); CALLOC(s->res, p->n_thread);
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kt_for(p->n_thread, worker_hap_ec_dbg_paf, s, (s->ei - s->si));
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destroy_ec_ovec_buf_t(s->buf);
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return s;
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} else if (step == 2) { // step 3: dump
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cal_ec_r_dbg_step_t *s = (cal_ec_r_dbg_step_t*)in; uint64_t k, z; bit_extz_t ez; memset(&ez, 0, sizeof(ez));
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// UC_Read qu; UC_Read tu; init_UC_Read(&qu); init_UC_Read(&tu);
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for (k = 0; k < p->n_thread; k++) {
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for (z = 0; z < s->res[k].n; z++) {
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ez.cigar.a = s->res[k].ec.a + s->res[k].a[z].bl; ez.cigar.n = ez.cigar.m = s->res[k].a[z].cc;
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// UC_Read_resize(qu, (s->res[k].a[z].qe - ((uint32_t)s->res[k].a[z].qns)));
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// recover_UC_Read_sub_region(qu.seq, ((uint32_t)s->res[k].a[z].qns), (s->res[k].a[z].qe - ((uint32_t)s->res[k].a[z].qns)), 0, &R_INF, (s->res[k].a[z].qns>>32));
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// UC_Read_resize(tu, (s->res[k].a[z].te - s->res[k].a[z].ts));
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// recover_UC_Read_sub_region(tu.seq, s->res[k].a[z].ts, s->res[k].a[z].te - s->res[k].a[z].ts, 0, &R_INF, s->res[k].a[z].tn);
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print_ov_dbg_paf(p->fp, NULL/**qu.seq**/, Get_NAME(R_INF, (s->res[k].a[z].qns>>32)), Get_NAME_LENGTH(R_INF, (s->res[k].a[z].qns>>32)),
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NULL/**tu.seq**/, Get_NAME(R_INF, (s->res[k].a[z].tn)), Get_NAME_LENGTH(R_INF, (s->res[k].a[z].tn)), (uint32_t)s->res[k].a[z].qns, s->res[k].a[z].qe, Get_READ_LENGTH(R_INF, (s->res[k].a[z].qns>>32)), s->res[k].a[z].ts, s->res[k].a[z].te, Get_READ_LENGTH(R_INF, (s->res[k].a[z].tn)), s->res[k].a[z].rev, &ez, cm);
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}
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free(s->res[k].a); free(s->res[k].ec.a);
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}
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free(s->res); free(s); ///destory_UC_Read(&qu); destory_UC_Read(&tu);
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}
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return 0;
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}
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void cal_ec_r_dbg(uint64_t n_thre, uint64_t n_a)
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{
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char *paf = NULL; MALLOC(paf, (strlen(asm_opt.output_file_name)+64));
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sprintf(paf, "%s.ovlp.paf", asm_opt.output_file_name);
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cal_ec_r_dbg_t sl; memset(&sl, 0, sizeof(sl));
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sl.n_thread = n_thre; sl.n_a = n_a; sl.chunk_size = 2000; sl.cn = 0; sl.fp = fopen(paf, "w");
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kt_pipeline(3, worker_ov_dbg_pipeline, &sl, 3);
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fclose(sl.fp); free(paf);
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}
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void destroy_cc_v(cc_v *z)
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{
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uint64_t k;
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@@ -15,5 +15,6 @@ void cal_ov_r(uint64_t n_thre, uint64_t n_a, uint64_t new_idx);
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void handle_chemical_r(uint64_t n_thre, uint64_t n_a);
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void handle_chemical_arc(uint64_t n_thre, uint64_t n_a);
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uint8_t* gen_chemical_arc_rf(uint64_t n_thre, uint64_t n_a);
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void cal_ec_r_dbg(uint64_t n_thre, uint64_t n_a);
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#endif
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@@ -62,7 +62,7 @@ int main(int argc, char *argv[])
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// ed_band_cal_global_128bit((char*)"ACTTTTTT", 8, (char*)"AATTTT", 6, 3));
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// exit(1);
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if(asm_opt.sec_in) ret = ha_assemble_pair();
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else if(asm_opt.dbg_ovec_cal) ret = ha_assemble_ovec();
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else if(asm_opt.dbg_ovec_cal) ret = ha_ec_dbg();
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else ret = ha_assemble();
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destory_opt(&asm_opt);
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