mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-02 12:28:11 +08:00
ont simplex support
This commit is contained in:
chhylp123
+501
-12
@@ -14,6 +14,56 @@
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#define del_cns_nn(z, nn_i) ((z).a[(nn_i)].sc == CNS_DEL_V)
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#define REFRESH_N 128
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KDQ_INIT(uint32_t)
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typedef struct {
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uint32_t v:31, f:1;
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uint32_t sc;
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} cns_arc;
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typedef struct {size_t n, m, nou; cns_arc *a; } cns_arc_v;
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typedef struct {
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// uint16_t c:2, t:2, f:1, sc:3;
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uint32_t c:2, f:1, sc:29;
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cns_arc_v arc;
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}cns_t;
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typedef struct {
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size_t n, m;
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cns_t *a;
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uint32_t si, ei, off, bn, bb0, bb1, cns_g_wl;
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kdq_t(uint32_t) *q;
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}cns_gfa;
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typedef struct {
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// chaining and overlapping related buffers
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UC_Read self_read, ovlp_read;
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Candidates_list clist;
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overlap_region_alloc olist;
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ha_abuf_t *ab;
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// int64_t num_read_base, num_correct_base, num_recorrect_base;
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uint64_t cnt[6], rr;
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haplotype_evdience_alloc hap;
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bit_extz_t exz;
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kv_ul_ov_t pidx;
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asg64_v v64;
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asg32_v v32;
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asg16_v v16;
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asg8_v v8q, v8t;
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kvec_t_u8_warp k_flag;
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st_mt_t sp;
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cns_gfa cns;
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} ec_ovec_buf_t0;
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typedef struct {
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ec_ovec_buf_t0 *a;
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uint32_t n, rev;
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} ec_ovec_buf_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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#define generic_key(x) (x)
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KRADIX_SORT_INIT(ec16, uint16_t, generic_key, 2)
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@@ -2608,6 +2658,7 @@ void push_ff_ovlp(ma_hit_t_alloc* paf, overlap_region_alloc* ov, uint32_t flag,
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if(z->el == 1) cnt[4]++;
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if(z->no_l_indel) cnt[5]++;
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}
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z->del = 0;
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}
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}
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@@ -2729,7 +2780,7 @@ inline uint64_t exact_ec_check(char *qstr, uint64_t ql, char *tstr, uint64_t tl,
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return 0;
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}
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void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rref, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t wl, int64_t rid, int64_t khit, int64_t move_gap, asg16_v *buf, asg64_v *srt, ma_hit_t_alloc *in)
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void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rref, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t wl, int64_t rid, int64_t khit, int64_t move_gap, asg16_v *buf, asg64_v *srt, ma_hit_t_alloc *in, uint8_t chem_drop)
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{
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if(ol->length <= 0) return;
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@@ -2744,7 +2795,7 @@ void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *
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}
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if(!(srt->n)) {
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gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf);
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gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop);
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} else {
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///debug for memory
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// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
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@@ -2778,7 +2829,7 @@ void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *
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///debug for memory
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// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
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if(on > nec) gen_hc_r_alin_nec(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf);
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if(on > nec) gen_hc_r_alin_nec(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop);
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///debug for memory
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// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
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@@ -2986,6 +3037,158 @@ void debug_retrive_bqual(asg8_v *vq, asg8_v *vt, uint64_t id, uint64_t rn)
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}
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}
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uint32_t is_uncorrected_read(overlap_region_alloc* ov, asg64_v *idx, int64_t len, int64_t min_len)
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{
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uint64_t k, s, e; int64_t dp, old_dp, st = 0, ed;
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for (k = idx->n = 0; k < ov->length; k++) {
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s = ov->list[k].x_pos_s; e = ov->list[k].x_pos_e + 1;
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kv_push(uint64_t, (*idx), (s<<1));
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kv_push(uint64_t, (*idx), (e<<1)|1);
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}
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radix_sort_ec64(idx->a, idx->a + idx->n);
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for (k = 0, dp = 0, st = ed = 0; k < idx->n; ++k) {
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old_dp = dp;
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///if a[j] is qe
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if (idx->a[k]&1) --dp;
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else ++dp;
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ed = idx->a[k]>>1;
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if(ed > st) {
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if(old_dp == 0) {
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if((ed - st) >= min_len) return 1;
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}
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}
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st = ed;
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}
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ed = len; old_dp = dp;
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if(ed > st) {
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if(old_dp == 0) {
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if((ed - st) >= min_len) return 1;
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if((ed - st) >= len) return 1;
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}
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}
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return 0;
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}
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uint32_t is_chemical_r_qual(overlap_region_alloc *ov, asg64_v *idx, int64_t len, int64_t cov, int64_t frank_len, asg8_v *qv, uint64_t rid)
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{
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uint64_t k, s, e; int64_t dp, old_dp, st = 0, ed, s0, s1, e0, e1, rr, qk;
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if((frank_len) > (len *0.01)) frank_len = len *0.01;
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for (k = idx->n = 0; k < ov->length; k++) {
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s = ov->list[k].x_pos_s; e = ov->list[k].x_pos_e + 1;
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kv_push(uint64_t, (*idx), (s<<1));
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kv_push(uint64_t, (*idx), (e<<1)|1);
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// fprintf(stderr, "[M::%s]\trid::%lu\ts::%lu\te::%lu\n", __func__, rid, s, e);
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}
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radix_sort_ec64(idx->a, idx->a + idx->n); s0 = s1 = e0 = e1 = rr = -1;
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for (k = 0, dp = 0, st = ed = 0; k < idx->n; ++k) {
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old_dp = dp;
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///if a[j] is qe
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if (idx->a[k]&1) --dp;
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else ++dp;
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ed = idx->a[k]>>1;
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if(ed > st) {
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if(old_dp <= cov) {
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rr = 1;
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} else {
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if(s0 < 0) {
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s0 = st; s1 = ed;
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}
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e0 = st; e1 = ed;
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}
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}
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st = ed;
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}
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ed = len; old_dp = dp;
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if(ed > st) {
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if(old_dp <= cov) {
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rr = 1;
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} else {
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if(s0 < 0) {
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s0 = st; s1 = ed;
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}
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e0 = st; e1 = ed;
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}
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}
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if((s0 != e0) && (s1 != e1) && (s0 <= frank_len) && ((len - e1) <= frank_len) && (rr > 0)) {
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for (k = 0, dp = 0, st = ed = 0; k < idx->n; ++k) {
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old_dp = dp;
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///if a[j] is qe
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if (idx->a[k]&1) --dp;
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else ++dp;
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ed = idx->a[k]>>1;
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if(ed > st) {
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if((old_dp <= cov) && (st >= s0) && (ed <= e1)) {
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retrive_bqual(qv, NULL, rid, -1, -1, 0, sc_bn);
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fprintf(stderr, "[M::%s]\tlf::[%ld,%ld)\trt::[%ld,%ld)\tmd::[%ld,%ld)\tcov::%ld\n", __func__, s0, s1, e0, e1, st, ed, old_dp);
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for (qk = st; qk < ed; qk++) fprintf(stderr, "%u", qv->a[qk]);
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fprintf(stderr, "\n");
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return 1;
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}
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}
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st = ed;
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}
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ed = len; old_dp = dp;
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if(ed > st) {
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if((old_dp <= cov) && (st >= s0) && (ed <= e1)) {
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retrive_bqual(qv, NULL, rid, -1, -1, 0, sc_bn);
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fprintf(stderr, "[M::%s]\tlf::[%ld,%ld)\trt::[%ld,%ld)\tmd::[%ld,%ld)\tcov::%ld\n", __func__, s0, s1, e0, e1, st, ed, old_dp);
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for (qk = st; qk < ed; qk++) fprintf(stderr, "%u", qv->a[qk]);
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fprintf(stderr, "\n");
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return 1;
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}
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}
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}
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// for (k = 0, dp = 0, st = ed = 0; k < idx->n; ++k) {
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// old_dp = dp;
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// ///if a[j] is qe
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// if (idx->a[k]&1) --dp;
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// else ++dp;
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// ed = idx->a[k]>>1;
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// if(ed > st) {
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// if((old_dp <= cov)) {
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// retrive_bqual(qv, NULL, rid, -1, -1, 0, sc_bn);
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// fprintf(stderr, "[M::%s]\tlf::[%ld,%ld)\trt::[%ld,%ld)\tmd::[%ld,%ld)\tcov::%ld\n", __func__, s0, s1, e0, e1, st, ed, old_dp);
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// for (qk = st; qk < ed; qk++) fprintf(stderr, "%u", qv->a[qk]);
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// fprintf(stderr, "\n");
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// return 1;
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// }
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// }
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// st = ed;
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// }
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// ed = len; old_dp = dp;
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// if(ed > st) {
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// if((old_dp <= cov)) {
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// retrive_bqual(qv, NULL, rid, -1, -1, 0, sc_bn);
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// fprintf(stderr, "[M::%s]\tlf::[%ld,%ld)\trt::[%ld,%ld)\tmd::[%ld,%ld)\tcov::%ld\n", __func__, s0, s1, e0, e1, st, ed, old_dp);
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// for (qk = st; qk < ed; qk++) fprintf(stderr, "%u", qv->a[qk]);
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// fprintf(stderr, "\n");
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// return 1;
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// }
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// }
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return 0;
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}
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static void worker_hap_ec(void *data, long i, int tid)
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{
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ec_ovec_buf_t0 *b = &(((ec_ovec_buf_t*)data)->a[tid]);
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@@ -3006,7 +3209,7 @@ static void worker_hap_ec(void *data, long i, int tid)
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// if(i % 100000 == 0) fprintf(stderr, "-a-[M::%s-beg] rid->%ld\n", __func__, i);
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// if (memcmp("c42804f3-0e13-43a0-8a71-b91b40accf9a", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
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// if (memcmp("b2e68ecf-381a-439c-b676-c1e6831d6acf", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
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// if (memcmp("0aec8c4f-c849-4c31-85ba-4ffb297eeb28", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
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// if (memcmp("64b2c27d-86b8-451e-9330-6ba62be2ffcc", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
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// fprintf(stderr, "-a-[M::%s-beg] rid->%ld\n", __func__, i);
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// } else {
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// return;
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@@ -3023,7 +3226,7 @@ static void worker_hap_ec(void *data, long i, int tid)
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recover_UC_Read(&b->self_read, &R_INF, i); qlen = b->self_read.length;
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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))**/0.02, asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 3, 0.7, 2, 32);///ONT high error
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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);///ONT high error
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// b->num_read_base += b->olist.length;
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b->cnt[0] += b->self_read.length;
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@@ -3033,7 +3236,7 @@ static void worker_hap_ec(void *data, long i, int tid)
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///debug for memory
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// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
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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/**asm_opt.k_mer_length**/, 1, &b->v16, &b->v64, &(R_INF.paf[i]));
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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/**asm_opt.k_mer_length**/, 1, &b->v16, &b->v64, &(R_INF.paf[i]), asm_opt.is_ont);
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// prt_ovlp_sam(&b->olist, &b->ovlp_read, b->self_read.seq, b->self_read.length);
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@@ -3061,7 +3264,10 @@ static void worker_hap_ec(void *data, long i, int tid)
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push_nec_re(aux_o, &(scc.a[i]));
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push_nec_re(aux_o, &(scb.a[i]));
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// if((asm_opt.is_ont) && is_chemical_r_qual(&b->olist, &b->v64, qlen, 1, 16, &(b->v8q), i)/**(is_uncorrected_read(&b->olist, &b->v64, qlen, 1600))**/) {
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// // b->olist.length = 0;
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// fprintf(stderr, "[M::%s] rid::%ld\t%.*s\n\n", __func__, i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
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// }
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push_ne_ovlp(&(R_INF.paf[i]), &b->olist, 1, &R_INF, &(scc.a[i])/**, i, &b->self_read, &b->ovlp_read**/);
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push_ne_ovlp(&(R_INF.reverse_paf[i]), &b->olist, 2, &R_INF, NULL/**, i, NULL, NULL**/);
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@@ -3605,9 +3811,9 @@ static void worker_hap_dc_ec_gen_new_idx(void *data, long i, int tid)
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ec_ovec_buf_t0 *b = &(((ec_ovec_buf_t*)data)->a[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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uint32_t low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO; uint32_t qlen = 0;
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recover_UC_Read(&b->self_read, &R_INF, i);
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recover_UC_Read(&b->self_read, &R_INF, i); qlen = b->self_read.length;
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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, /**0.02**/0.001, asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 3, 0.7, 2, 32);
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@@ -3624,6 +3830,11 @@ static void worker_hap_dc_ec_gen_new_idx(void *data, long i, int tid)
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h_ec_lchain_fast_new(b->ab, i, &b->self_read, &b->ovlp_read, &R_INF, &b->olist, &b->clist, &b->exz, &b->v16, &b->v64, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), 0.866666);
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if((asm_opt.is_ont) && (is_uncorrected_read(&b->olist, &b->v64, qlen, 1600))) {
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b->olist.length = 0;
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// fprintf(stderr, "[M::%s] rid::%ld\t%.*s\n", __func__, i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
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}
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push_ff_ovlp(&(R_INF.paf[i]), &b->olist, 1, &R_INF, b->cnt);
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push_ff_ovlp(&(R_INF.reverse_paf[i]), &b->olist, 2, &R_INF, b->cnt);
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@@ -3641,6 +3852,236 @@ static void worker_hap_dc_ec_gen_new_idx(void *data, long i, int tid)
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refresh_ec_ovec_buf_t0(b, REFRESH_N);
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}
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|
||||
uint32_t is_chemical_r(ma_hit_t_alloc *ov, asg64_v *idx, int64_t len, int64_t cov, int64_t frank_len)
|
||||
{
|
||||
uint64_t k, s, e; int64_t dp, old_dp, st = 0, ed, s0, s1, e0, e1, rr;
|
||||
if((frank_len) > (len *0.01)) frank_len = len *0.01;
|
||||
for (k = idx->n = 0; k < ov->length; k++) {
|
||||
s = (uint32_t)ov->buffer[k].qns; e = ov->buffer[k].qe;
|
||||
kv_push(uint64_t, (*idx), (s<<1));
|
||||
kv_push(uint64_t, (*idx), (e<<1)|1);
|
||||
}
|
||||
|
||||
radix_sort_ec64(idx->a, idx->a + idx->n); s0 = s1 = e0 = e1 = rr = -1;
|
||||
for (k = 0, dp = 0, st = ed = 0; k < idx->n; ++k) {
|
||||
old_dp = dp;
|
||||
///if a[j] is qe
|
||||
if (idx->a[k]&1) --dp;
|
||||
else ++dp;
|
||||
|
||||
ed = idx->a[k]>>1;
|
||||
if(ed > st) {
|
||||
if(old_dp <= cov) {
|
||||
rr = 1;
|
||||
} else {
|
||||
if(s0 < 0) {
|
||||
s0 = st; s1 = ed;
|
||||
}
|
||||
e0 = st; e1 = ed;
|
||||
}
|
||||
}
|
||||
st = ed;
|
||||
}
|
||||
|
||||
|
||||
ed = len; old_dp = dp;
|
||||
if(ed > st) {
|
||||
if(old_dp <= cov) {
|
||||
rr = 1;
|
||||
} else {
|
||||
if(s0 < 0) {
|
||||
s0 = st; s1 = ed;
|
||||
}
|
||||
e0 = st; e1 = ed;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if((s0 != e0) && (s1 != e1) && (s0 <= frank_len) && ((len - e1) <= frank_len) && (rr > 0)) {
|
||||
for (k = 0, dp = 0, st = ed = 0; k < idx->n; ++k) {
|
||||
old_dp = dp;
|
||||
///if a[j] is qe
|
||||
if (idx->a[k]&1) --dp;
|
||||
else ++dp;
|
||||
|
||||
ed = idx->a[k]>>1;
|
||||
if(ed > st) {
|
||||
if((old_dp <= cov) && (st >= s0) && (ed <= e1)) {
|
||||
// if((ov->buffer[0].qns>>32) == 3364) fprintf(stderr, "[M::%s]\tlf::[%ld,%ld)\trt::[%ld,%ld)\tmd::[%ld,%ld)\tcov::%ld\n", __func__, s0, s1, e0, e1, st, ed, old_dp);
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
st = ed;
|
||||
}
|
||||
|
||||
|
||||
ed = len; old_dp = dp;
|
||||
if(ed > st) {
|
||||
if((old_dp <= cov) && (st >= s0) && (ed <= e1)) {
|
||||
// if((ov->buffer[0].qns>>32) == 3364) fprintf(stderr, "[M::%s]\tlf::[%ld,%ld)\trt::[%ld,%ld)\tmd::[%ld,%ld)\tcov::%ld\n", __func__, s0, s1, e0, e1, st, ed, old_dp);
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
uint32_t is_chemical_r_adv(ma_hit_t_alloc *ov, asg64_v *idx, int64_t len, int64_t cov, int64_t cut_len, double dup_rate)
|
||||
{
|
||||
uint64_t k, s, e; int64_t dp, old_dp, st = 0, ed, s0, e0, rr, lt;
|
||||
for (k = idx->n = 0; k < ov->length; k++) {
|
||||
s0 = (uint32_t)ov->buffer[k].qns; e0 = ov->buffer[k].qe;
|
||||
if(s0 > 0) s0 += cut_len;
|
||||
if(e0 < len) e0 -= cut_len;
|
||||
if(e0 <= s0) continue;
|
||||
s = s0; e = e0;
|
||||
|
||||
lt = Get_READ_LENGTH((R_INF), ov->buffer[k].tn);
|
||||
rr = (lt >= len)?(lt - len):(len - lt);
|
||||
if((rr <= (len*dup_rate)) && (rr <= (lt*dup_rate)) && (ov->buffer[k].rev)) {
|
||||
dp = (ov->buffer[k].qe) - ((uint32_t)ov->buffer[k].qns); dp = len - dp;
|
||||
old_dp = ov->buffer[k].te - ov->buffer[k].ts; old_dp = lt - old_dp;
|
||||
if((dp <= (len*dup_rate)) && (old_dp <= (lt*dup_rate))) continue;
|
||||
}
|
||||
|
||||
kv_push(uint64_t, (*idx), (s<<1));
|
||||
kv_push(uint64_t, (*idx), (e<<1)|1);
|
||||
}
|
||||
|
||||
radix_sort_ec64(idx->a, idx->a + idx->n); s0 = e0 = rr = -1;
|
||||
for (k = 0, dp = 0, st = ed = 0; k < idx->n; ++k) {
|
||||
old_dp = dp;
|
||||
///if a[j] is qe
|
||||
if (idx->a[k]&1) --dp;
|
||||
else ++dp;
|
||||
|
||||
ed = idx->a[k]>>1;
|
||||
if(ed > st) {
|
||||
// if(ov->length && ((ov->buffer[0].qns>>32) == 5045637)) {
|
||||
// fprintf(stderr, "[M::%s]\tmd::[%ld,%ld)\tcov::%ld\tlen::%ld\tid::%lu\n", __func__, st, ed, old_dp, len, ov->buffer[0].qns>>32);
|
||||
// }
|
||||
if(old_dp <= cov) {
|
||||
// if(ov->length && (ov->buffer[0].qns>>32) == 22344) fprintf(stderr, "[M::%s]\tmd::[%ld,%ld)\tcov::%ld\tlen::%ld\n", __func__, st, ed, old_dp, len);
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
st = ed;
|
||||
}
|
||||
|
||||
|
||||
ed = len; old_dp = dp;
|
||||
if(ed > st) {
|
||||
// if(ov->length && ((ov->buffer[0].qns>>32) == 5045637)) {
|
||||
// fprintf(stderr, "[M::%s]\tmd::[%ld,%ld)\tcov::%ld\tlen::%ld\tid::%lu\n", __func__, st, ed, old_dp, len, ov->buffer[0].qns>>32);
|
||||
// }
|
||||
if(old_dp <= cov) {
|
||||
// if(ov->length && (ov->buffer[0].qns>>32) == 22344) fprintf(stderr, "[M::%s]\tmd::[%ld,%ld)\tcov::%ld\tlen::%ld\n", __func__, st, ed, old_dp, len);
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
void prt_dbg_rid_paf(ma_hit_t_alloc *ov, UC_Read *ra, asg8_v *qa)
|
||||
{
|
||||
if(!(ov->length)) return;
|
||||
uint64_t k, qn = (ov->buffer[0].qns>>32), qn_n, i, m; char *nn = NULL; FILE *fp = NULL; ma_hit_t *h = NULL;
|
||||
qn_n = Get_NAME_LENGTH((R_INF), qn) + 64; MALLOC(nn, qn_n);
|
||||
|
||||
sprintf(nn, "%.*s.qry.fq", (int)Get_NAME_LENGTH(R_INF, qn), Get_NAME((R_INF), qn)); fp = fopen(nn, "w");
|
||||
for (k = 0; k < ov->length; k++) {
|
||||
i = ov->buffer[k].tn;
|
||||
recover_UC_Read(ra, &R_INF, i);
|
||||
fprintf(fp, "@%.*s\n", (int32_t)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
|
||||
fprintf(fp, "%.*s\n", (int32_t)ra->length, ra->seq);
|
||||
fprintf(fp, "+\n");
|
||||
retrive_bqual(qa, NULL, i, -1, -1, 0, sc_bn);
|
||||
for (m = 0; m < qa->n; m++) fprintf(fp, "%c", (char)(sc_tb[qa->a[m]] + 33 - 1));
|
||||
fprintf(fp, "\n");
|
||||
}
|
||||
fclose(fp);
|
||||
|
||||
sprintf(nn, "%.*s.ref.fq", (int)Get_NAME_LENGTH(R_INF, qn), Get_NAME((R_INF), qn)); fp = fopen(nn, "w");
|
||||
i = qn;
|
||||
recover_UC_Read(ra, &R_INF, i);
|
||||
fprintf(fp, "@%.*s\n", (int32_t)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
|
||||
fprintf(fp, "%.*s\n", (int32_t)ra->length, ra->seq);
|
||||
fprintf(fp, "+\n");
|
||||
retrive_bqual(qa, NULL, i, -1, -1, 0, sc_bn);
|
||||
for (m = 0; m < qa->n; m++) fprintf(fp, "%c", (char)(sc_tb[qa->a[m]] + 33 - 1));
|
||||
fprintf(fp, "\n");
|
||||
fclose(fp);
|
||||
|
||||
sprintf(nn, "%.*s.ref.fa", (int)Get_NAME_LENGTH(R_INF, qn), Get_NAME((R_INF), qn)); fp = fopen(nn, "w");
|
||||
i = qn;
|
||||
recover_UC_Read(ra, &R_INF, i);
|
||||
fprintf(fp, ">%.*s\n", (int32_t)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
|
||||
fprintf(fp, "%.*s\n", (int32_t)ra->length, ra->seq);
|
||||
// fprintf(fp, "+\n");
|
||||
// retrive_bqual(qa, NULL, i, -1, -1, 0, sc_bn);
|
||||
// for (m = 0; m < qa->n; m++) fprintf(fp, "%c", (char)(sc_tb[qa->a[m]] + 33 - 1));
|
||||
// fprintf(fp, "\n");
|
||||
fclose(fp);
|
||||
|
||||
sprintf(nn, "%.*s.ov.paf", (int)Get_NAME_LENGTH(R_INF, qn), Get_NAME((R_INF), qn)); fp = fopen(nn, "w");
|
||||
for (k = 0; k < ov->length; k++) {
|
||||
h = &(ov->buffer[k]);
|
||||
fprintf(fp, "%.*s(qn::%u)\t%u\t%u\t%u\t%c\t%.*s(tn::%u)\t%u\t%u\t%u\t%u\t%u\t255\n", (int)Get_NAME_LENGTH(R_INF, Get_qn(*h)), Get_NAME((R_INF), Get_qn(*h)), Get_qn(*h), (uint32_t)Get_READ_LENGTH(R_INF, Get_qn(*h)), Get_qs(*h), Get_qe(*h), "+-"[h->rev],
|
||||
(int)Get_NAME_LENGTH(R_INF, Get_tn(*h)), Get_NAME((R_INF), Get_tn(*h)), Get_tn(*h), (uint32_t)Get_READ_LENGTH(R_INF, Get_tn(*h)), Get_ts(*h), Get_te(*h), h->ml, h->bl);
|
||||
}
|
||||
fclose(fp);
|
||||
|
||||
free(nn);
|
||||
}
|
||||
|
||||
static void worker_hap_dc_ec_chemical_r(void *data, long i, int tid)
|
||||
{
|
||||
ec_ovec_buf_t0 *b = &(((ec_ovec_buf_t*)data)->a[tid]);
|
||||
ma_hit_t_alloc *paf = &(R_INF.paf[i]); uint64_t k, m;
|
||||
|
||||
// if (memcmp("3ed80bc4-1169-4948-a9ff-9c2463b7f7a2", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
|
||||
// fprintf(stderr, "-a-[M::%s-beg] rid->%ld, b->rr->%lu\n", __func__, i, b->rr);
|
||||
// }
|
||||
if(b->cnt[1] == 0) {
|
||||
// if(i == 6204620) prt_dbg_rid_paf(&(R_INF.paf[i]), &(b->self_read), &(b->v8q));
|
||||
// if(is_chemical_r(&(R_INF.paf[i]), &b->v64, Get_READ_LENGTH((R_INF), i), 3, 16)) {
|
||||
if(is_chemical_r_adv(&(R_INF.paf[i]), &b->v64, Get_READ_LENGTH((R_INF), i), asm_opt.chemical_cov, asm_opt.chemical_flank, 0.02)) {
|
||||
// fprintf(stderr, "-um-[M::%s]\tqn::%u::%.*s\n\n", __func__, (uint32_t)(i), (int)Get_NAME_LENGTH(R_INF, i), Get_NAME((R_INF), i));
|
||||
R_INF.paf[i].length = 0; b->cnt[0]++;
|
||||
}
|
||||
} else if(b->cnt[1] == 1) {
|
||||
for (k = 0; k < paf->length; k++) {
|
||||
if(R_INF.paf[paf->buffer[k].tn].length == 0) {
|
||||
paf->buffer[k].tn = (uint32_t)-1; b->cnt[0]++;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (k = m = 0; k < paf->length; k++) {
|
||||
if(paf->buffer[k].tn == ((uint32_t)-1)) continue;
|
||||
paf->buffer[m++] = paf->buffer[k];
|
||||
}
|
||||
paf->length = m;
|
||||
}
|
||||
|
||||
refresh_ec_ovec_buf_t0(b, REFRESH_N);
|
||||
}
|
||||
|
||||
static void worker_hap_dc_ec_chemical_arc(void *data, long i, int tid)
|
||||
{
|
||||
ec_ovec_buf_t0 *b = &(((ec_ovec_buf_t*)data)->a[tid]);
|
||||
ma_hit_t_alloc *paf = &(R_INF.paf[i]); uint64_t k;
|
||||
|
||||
if(is_chemical_r_adv(&(R_INF.paf[i]), &b->v64, Get_READ_LENGTH((R_INF), i), asm_opt.chemical_cov, asm_opt.chemical_flank, 0.02)) {
|
||||
// fprintf(stderr, "-um-[M::%s]\tqn::%u::%.*s\n\n", __func__, (uint32_t)(i), (int)Get_NAME_LENGTH(R_INF, i), Get_NAME((R_INF), i));
|
||||
for (k = 0; k < paf->length; k++) paf->buffer[k].del = 1; b->cnt[0]++;
|
||||
}
|
||||
|
||||
refresh_ec_ovec_buf_t0(b, REFRESH_N);
|
||||
}
|
||||
|
||||
void gen_ovlst_paf(ma_hit_t_alloc *in_e, ma_hit_t_alloc *in_r, asg64_v *ou)
|
||||
{
|
||||
uint32_t n = 0, k;
|
||||
@@ -3843,7 +4284,7 @@ overlap_region* h_ec_lchain_re1(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Rea
|
||||
|
||||
// fprintf(stderr, "-0-[M::%s]\n", __func__);
|
||||
|
||||
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, asm_opt.max_ov_diff_ec, w.window_length, rid, E_KHIT, 1, buf); rs = qu->seq;
|
||||
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, asm_opt.max_ov_diff_ec, w.window_length, rid, E_KHIT, 1, buf, 0); rs = qu->seq;
|
||||
|
||||
// fprintf(stderr, "-1-[M::%s]\n", __func__);
|
||||
|
||||
@@ -4507,7 +4948,7 @@ overlap_region* h_ec_lchain_re3(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Rea
|
||||
|
||||
// fprintf(stderr, "-0-[M::%s]\n", __func__);
|
||||
|
||||
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, asm_opt.max_ov_diff_ec, w.window_length, rid, E_KHIT, 1, buf); rs = qu->seq;
|
||||
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, asm_opt.max_ov_diff_ec, w.window_length, rid, E_KHIT, 1, buf, 0); rs = qu->seq;
|
||||
|
||||
// fprintf(stderr, "-1-[M::%s]\n", __func__);
|
||||
|
||||
@@ -5588,7 +6029,55 @@ void sl_ec_r(uint64_t n_thre, uint64_t n_a)
|
||||
kt_for(n_thre, worker_sl_ec, b, n_a);///debug_for_fix
|
||||
|
||||
for (k = 0; k < n_thre; k++) {
|
||||
free(b[k].a); destory_UC_Read(&b[k].z);
|
||||
free(b[k].a); destory_UC_Read(&b[k].z); kv_destroy(b[k].q);
|
||||
}
|
||||
free(b);
|
||||
}
|
||||
|
||||
void handle_chemical_r(uint64_t n_thre, uint64_t n_a)
|
||||
{
|
||||
ec_ovec_buf_t *b = NULL; uint64_t k, chem_n = 0, dedup = 0;
|
||||
b = gen_ec_ovec_buf_t(n_thre);
|
||||
for (k = 0; k < n_thre; ++k) {
|
||||
b->a[k].cnt[0] = 0; b->a[k].cnt[1] = 0;
|
||||
}
|
||||
|
||||
kt_for(n_thre, worker_hap_dc_ec_chemical_r, b, n_a);
|
||||
|
||||
for (k = 0; k < n_thre; ++k) {
|
||||
chem_n += b->a[k].cnt[0];
|
||||
b->a[k].cnt[0] = 0; b->a[k].cnt[1] = 1;
|
||||
}
|
||||
|
||||
kt_for(n_thre, worker_hap_dc_ec_chemical_r, b, n_a);
|
||||
|
||||
for (k = 0; k < n_thre; ++k) {
|
||||
dedup += b->a[k].cnt[0];
|
||||
b->a[k].cnt[1] = 2;
|
||||
}
|
||||
|
||||
kt_for(n_thre, worker_hap_dc_ec_chemical_r, b, n_a);
|
||||
|
||||
fprintf(stderr, "[M::%s] # chemical reads: %lu, # arcs:: %lu\n", __func__, chem_n, dedup);
|
||||
|
||||
destroy_ec_ovec_buf_t(b);
|
||||
}
|
||||
|
||||
void handle_chemical_arc(uint64_t n_thre, uint64_t n_a)
|
||||
{
|
||||
ec_ovec_buf_t *b = NULL; uint64_t k, chem_n = 0;
|
||||
b = gen_ec_ovec_buf_t(n_thre);
|
||||
for (k = 0; k < n_thre; ++k) {
|
||||
b->a[k].cnt[0] = 0;
|
||||
}
|
||||
|
||||
kt_for(n_thre, worker_hap_dc_ec_chemical_arc, b, n_a);
|
||||
|
||||
for (k = 0; k < n_thre; ++k) {
|
||||
chem_n += b->a[k].cnt[0];
|
||||
}
|
||||
|
||||
fprintf(stderr, "[M::%s] # chemical reads: %lu\n", __func__, chem_n);
|
||||
|
||||
destroy_ec_ovec_buf_t(b);
|
||||
}
|
||||
Reference in New Issue
Block a user