Merge pull request #411 from chhylp123/hifiasm_dev_debug

bug fixed for mask calculation

CommandLines.h

@@ -5,7 +5,7 @@
 #include <pthread.h>
 #include <stdint.h>
 
-#define HA_VERSION "0.18.8-r525"
+#define HA_VERSION "0.18.9-r527"
 
 #define VERBOSE 0
 

Correct.cpp

@@ -18617,7 +18617,18 @@ void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
  if(ol->length <= 0) return;
  } else {
  // fprintf(stderr, "-[M::%s] on::%lu\n", __func__, ol->length);
- if(ol->length <= 1) return;
+ if(ol->length <= 1) {
+ if(ol->length == 1) {
+ window_list *p;
+ z = &(ol->list[0]); z->w_list.n = 0;
+ kv_pushp(window_list, z->w_list, &p);
+ memset(p, 0, sizeof((*p)));
+ p->x_start = z->x_pos_s; p->x_end = z->x_pos_e+1; p->clen = 0;
+ z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s;
+ z->non_homopolymer_errors = 0;
+ }
+ return;
+ }
  ///coordinates for all intervals with cov > 1
  copy_asg_arr(iidx, hap->snp_srt); copy_asg_arr(buf, v_idx->a); copy_asg_arr(buf1, (*stb));
  // fprintf(stderr, "\n[M::%s] iidx_n::%ld\n", __func__, (int64_t)iidx.n);
@@ -21022,7 +21033,7 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t
  int64_t aux_n = aux_o->w_list.n;
 
 
- // if(z->x_id == 29033 && z->y_id == 21307) {
+ // if(z->x_id == 77960 && z->y_id == 27340) {
  // fprintf(stderr, "\n[M::%s]\tutg%.6u%c\txl::%u\tx::[%u,\t%u)\t%c\tutg%.6u%c\tyl::%u\ty::[%u,\t%u)\n", 
  // __func__, 
  // z->x_id+1, "lc"[udb->ug->u.a[z->x_id].circ], udb->ug->u.a[z->x_id].len, z->x_pos_s, z->x_pos_e+1,
@@ -21046,7 +21057,7 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t
  rechain_aln(z, cl, aux_o, i, w_l, udb, NULL, NULL, qstr, tu, exz, e_rate, ql, tl, khit, rid);
  }
 
- // if(z->x_id == 29033 && z->y_id == 21307) {
+ // if(z->x_id == 77960 && z->y_id == 27340) {
  // fprintf(stderr, "\n[M::%s]\tutg%.6u%c\txl::%u\tx::[%u,\t%u)\t%c\tutg%.6u%c\tyl::%u\ty::[%u,\t%u)\n", 
  // __func__, 
  // z->x_id+1, "lc"[udb->ug->u.a[z->x_id].circ], udb->ug->u.a[z->x_id].len, z->x_pos_s, z->x_pos_e+1,
@@ -21086,7 +21097,7 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t
  }
  z->non_homopolymer_errors = zerr;
 
- // if(z->x_id == 29033 && z->y_id == 21307) {
+ // if(z->x_id == 77960 && z->y_id == 27340) {
  // fprintf(stderr, "\n[M::%s]\tutg%.6u%c\txl::%u\tx::[%u,\t%u)\t%c\tutg%.6u%c\tyl::%u\ty::[%u,\t%u)\n", 
  // __func__, 
  // z->x_id+1, "lc"[udb->ug->u.a[z->x_id].circ], udb->ug->u.a[z->x_id].len, z->x_pos_s, z->x_pos_e+1,
@@ -21308,12 +21319,13 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
  rr = gen_extend_err_exz(z, uref, NULL, NULL, in/**qu->seq**/, tu->seq, exz, NULL/**v_idx?v_idx->a.a:NULL**/, w.window_length, -1, err, (e_max+0.000001), &re);
  z->is_match = 0;///must be here;
 
- // if(sid == 7 && z->y_id == 135) {
- // fprintf(stderr, "===utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\talign_length::%u\terr::%f\trr::%f\twn::%u\n", 
+ // if(z->x_id == 77960 && z->y_id == 27340) { 
+ // fprintf(stderr, "+utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\talign_length::%u\terr::%f\trr::%f\twn::%u\tk::%lu\ti::%lu\n", 
  // z->x_id+1, "lc"[uref->ug->u.a[z->x_id].circ], uref->ug->u.a[z->x_id].len, 
  // z->x_pos_s, z->x_pos_e+1, "+-"[z->y_pos_strand],
  // z->y_id+1, "lc"[uref->ug->u.a[z->y_id].circ], uref->ug->u.a[z->y_id].len, 
- // z->y_pos_s, z->y_pos_e+1, z->align_length, err, rr, (uint32_t)z->w_list.n/**gen_nkhits(cl, z)**/);
+ // z->y_pos_s, z->y_pos_e+1, z->align_length, err, rr, (uint32_t)z->w_list.n/**gen_nkhits(cl, z)**/,
+ // k, i);
  // }
  if (rr <= err) {
  if(k != i) {
@@ -21327,18 +21339,39 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
  }
 
  ol->length = k;
+ // if(sid == 77960) { 
+ // fprintf(stderr, "+utg%.6ld%c\tol->length::%lu\n", sid+1, "lc"[uref->ug->u.a[sid].circ], ol->length);
+ // }
  if(ol->length <= 0) return;
  } else {
- if(ol->length <= 1) return;
+ // if(ol->length <= 1) return;
+ if(ol->length <= 0) return;
  if(qu) {
  resize_UC_Read(qu, ql); qu->length = ql; memcpy(qu->seq, qstr, ql); in = qu->seq;
  } 
  for (i = k = 0; i < ol->length; i++) {
  z = &(ol->list[i]); 
+ // if(z->x_id == 77960 && z->y_id == 27340) { 
+ // fprintf(stderr, "-1-utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\talign_length::%u\terr::%f\twn::%u\tk::%lu\ti::%lu\n", 
+ // z->x_id+1, "lc"[uref->ug->u.a[z->x_id].circ], uref->ug->u.a[z->x_id].len, 
+ // z->x_pos_s, z->x_pos_e+1, "+-"[z->y_pos_strand],
+ // z->y_id+1, "lc"[uref->ug->u.a[z->y_id].circ], uref->ug->u.a[z->y_id].len, 
+ // z->y_pos_s, z->y_pos_e+1, z->align_length, err, (uint32_t)z->w_list.n/**gen_nkhits(cl, z)**/,
+ // k, i);
+ // }
  if(!ul_raw_aln(z, cl, uref, in/**qu->seq**/, tu, exz, err, wl, ql, sid, khit, aux_o)) {
  z->is_match = 0;
  continue;
  }
+
+ // if(z->x_id == 77960 && z->y_id == 27340) { 
+ // fprintf(stderr, "-2-utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\talign_length::%u\terr::%f\twn::%u\tk::%lu\ti::%lu\n", 
+ // z->x_id+1, "lc"[uref->ug->u.a[z->x_id].circ], uref->ug->u.a[z->x_id].len, 
+ // z->x_pos_s, z->x_pos_e+1, "+-"[z->y_pos_strand],
+ // z->y_id+1, "lc"[uref->ug->u.a[z->y_id].circ], uref->ug->u.a[z->y_id].len, 
+ // z->y_pos_s, z->y_pos_e+1, z->align_length, err, (uint32_t)z->w_list.n/**gen_nkhits(cl, z)**/,
+ // k, i);
+ // }
  if(k != i) {
  t = ol->list[k];
  ol->list[k] = ol->list[i];
@@ -21348,5 +21381,9 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
  k++;
  }
  ol->length = k;
+
+ // if(sid == 77960) { 
+ // fprintf(stderr, "-utg%.6ld%c\tol->length::%lu\n", sid+1, "lc"[uref->ug->u.a[sid].circ], ol->length);
+ // }
  }
 }

inter.cpp

@@ -11228,7 +11228,7 @@ int64_t cal_exact_batch(overlap_region *z, ul_ov_t *sa, uint64_t sn, int64_t yle
  }
 
  if((*q0l) >= (z->x_pos_e+1-z->x_pos_s) && (*t0l) >= (z->y_pos_e+1-z->y_pos_s)) {
- // if((!(((*q0l) == (*q1l)) && ((*t0l) == (*t1l)) && (err0 == err1))) || (!(err0 == tot))) {
+ // if((!(((*q0l) == (*q1l)) && ((*t0l) == (*t1l)) && (err0 == err1)))/** || (!(err0 == tot))**/) {
  // fprintf(stderr, "[M::%s]\tutg%.6u%c\txl::%u\tx::[%u,\t%u)\t%c\tutg%.6u%c\tyl::%u\ty::[%u,\t%u)\terr::%u\twn::%u\n", 
  // __func__, 
  // z->x_id+1, "lc"[ug->u.a[z->x_id].circ], ug->u.a[z->x_id].len, z->x_pos_s, z->x_pos_e+1,
@@ -11703,6 +11703,8 @@ static void worker_for_graph_bin(void *data, long i, int tid) // callback for kt
  seq = b->self_read.seq;
  }
 
+ // if(i!=77960) return;
+
  // asprintf(&as, "\n[M::%s] rid::%ld, len::%lu, name::%.*s\n", __func__, s->id+i, s->len[i], (int32_t)UL_INF.nid.a[s->id+i].n, UL_INF.nid.a[s->id+i].a);
  // push_vlog(&(overall_zdbg->a[s->id+i]), as); free(as); as = NULL;