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bug fixed for mask calculation

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chhylp123
2023-02-24 00:36:52 -05:00
parent 2b4b4f29e0
commit 04f660fd8c
3 changed files with 49 additions and 10 deletions
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CommandLines.h
+1 -1
View File
@@ -5,7 +5,7 @@
#include <pthread.h> #include <pthread.h>
#include <stdint.h> #include <stdint.h>
#define HA_VERSION "0.18.8-r525" #define HA_VERSION "0.18.9-r527"
#define VERBOSE 0 #define VERBOSE 0
Correct.cpp
+45 -8
View File
@@ -18617,7 +18617,18 @@ void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
if(ol->length <= 0) return; if(ol->length <= 0) return;
} else { } else {
// fprintf(stderr, "-[M::%s] on::%lu\n", __func__, ol->length); // 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 ///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)); 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); // 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; 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", // 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__, // __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, // 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); 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", // 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__, // __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, // 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; 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", // 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__, // __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, // 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); 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; z->is_match = 0;///must be here;
// if(sid == 7 && z->y_id == 135) { // 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\n", // 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_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->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_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 (rr <= err) {
if(k != i) { 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; 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; if(ol->length <= 0) return;
} else { } else {
if(ol->length <= 1) return; // if(ol->length <= 1) return;
if(ol->length <= 0) return;
if(qu) { if(qu) {
resize_UC_Read(qu, ql); qu->length = ql; memcpy(qu->seq, qstr, ql); in = qu->seq; resize_UC_Read(qu, ql); qu->length = ql; memcpy(qu->seq, qstr, ql); in = qu->seq;
} }
for (i = k = 0; i < ol->length; i++) { for (i = k = 0; i < ol->length; i++) {
z = &(ol->list[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)) { if(!ul_raw_aln(z, cl, uref, in/**qu->seq**/, tu, exz, err, wl, ql, sid, khit, aux_o)) {
z->is_match = 0; z->is_match = 0;
continue; 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) { if(k != i) {
t = ol->list[k]; t = ol->list[k];
ol->list[k] = ol->list[i]; 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++; k++;
} }
ol->length = 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
+3 -1
View File
@@ -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) >= (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", // 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__, // __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, // 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; 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); // 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; // push_vlog(&(overall_zdbg->a[s->id+i]), as); free(as); as = NULL;