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chhylp123
2022-11-01 21:44:13 -04:00
parent f4b6223fde
commit e66c003b65
6 changed files with 666 additions and 183 deletions
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Correct.cpp
+136 -83
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@@ -15027,7 +15027,8 @@ UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql,
// fprintf(stderr, "\n[M::%s::rid->%ld] utg%.6dl(%c), z::[%u, %u)\n",
// __func__, rid, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], z->x_pos_s, z->x_pos_e+1);
on = fusion_chain_ovlp(z, ch_a, ch_n, ov, on, wl, ql, tl);
aux_o->w_list.n = 0; aux_o->y_id = z->y_id; aux_o->y_pos_strand = z->y_pos_strand;
aux_o->w_list.n = aux_o->w_list.c.n = 0;
aux_o->y_id = z->y_id; aux_o->y_pos_strand = z->y_pos_strand;
aux_o->x_pos_s = z->x_pos_s; aux_o->x_pos_e = z->x_pos_e;
aux_o->y_pos_s = z->y_pos_s; aux_o->y_pos_e = z->y_pos_e;
@@ -15145,7 +15146,8 @@ UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql,
// fprintf(stderr, "\n[M::%s::rid->%ld] utg%.6dl(%c), z::[%u, %u)\n",
// __func__, rid, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], z->x_pos_s, z->x_pos_e+1);
on = fusion_chain_ovlp(z, ch_a, ch_n, ov, on, wl, ql, tl);
aux_o->w_list.n = 0; aux_o->y_id = z->y_id; aux_o->y_pos_strand = z->y_pos_strand;
aux_o->w_list.n = aux_o->w_list.c.n = 0;
aux_o->y_id = z->y_id; aux_o->y_pos_strand = z->y_pos_strand;
aux_o->x_pos_s = z->x_pos_s; aux_o->x_pos_e = z->x_pos_e;
aux_o->y_pos_s = z->y_pos_s; aux_o->y_pos_e = z->y_pos_e;
@@ -15331,61 +15333,102 @@ uint64_t query_gen_gov_idx(asg64_v *ovidx, uint64_t v, uint64_t w)
return 0;
}
void push_sec_aln(overlap_region *z, int64_t s, int64_t e, int64_t sec_err)
{
window_list *p;
if(z->align_length > 0) {
p = z->w_list.a + z->w_list.n + z->align_length - 1;
if((p->x_end == s) && ((!!(p->clen)) == (!!sec_err))) {
p->x_end = e; p->clen += sec_err;
return;
}
}
if((z->w_list.n+z->align_length)==z->w_list.m) {
z->w_list.m = z->w_list.m? z->w_list.m<<1 : 2;
z->w_list.a = (window_list*)realloc(z->w_list.a, sizeof(window_list)*z->w_list.m);
}
p = &(z->w_list.a[z->w_list.n+z->align_length]); z->align_length++; memset(p, 0, sizeof((*p)));
p->x_start = s; p->x_end = e; p->clen += sec_err;
}
// #define id_mm ((uint64_t)0x7fffffffffffffff)
#define id_set ((uint64_t)0x8000000000000000)
#define id_get(a) ((uint32_t)(a))
#define err_get(a) (((a)&((uint64_t)0x7fffffffffffffff))>>32)
void reassign_sec_err(overlap_region* ol, asg64_v *ovidx, asg64_v *buf, uint64_t bid0)
{
uint64_t bn = buf->n, bid = bid0, oid, mid, m, s, e;
if(buf->a[bid]&id_set) return;
kv_push(uint64_t, *buf, bid);
while (buf->n > bn) {
bid = buf->a[--buf->n];
if(buf->a[bid]&id_set) continue;
buf->a[bid]|=id_set;
oid = id_get(buf->a[bid]);
s = ovidx->a[oid]>>32; e = (uint32_t)ovidx->a[oid];
for (m = s; m < e; m++) {
mid = ol[(uint32_t)ovidx->a[m]].overlapLen;
if(mid == (uint32_t)-1) continue;
if(buf->a[mid]&id_set) continue;
kv_push(uint64_t, *buf, mid);
}
}
}
///[s, e)
uint64_t gen_region_phase(overlap_region* ol, uint64_t *id_a, uint64_t id_n, uint64_t s, uint64_t e, uint64_t dp, ul_ov_t *c_idx, uint64_t *buf, asg64_v *ovidx)
uint64_t gen_region_phase(overlap_region* ol, uint64_t *id_a, uint64_t id_n, uint64_t s, uint64_t e, uint64_t dp, ul_ov_t *c_idx, asg64_v *buf, asg64_v *ovidx)
{
if(!id_n) return id_n;
uint64_t k, m, mn, q[2], buf_n, rm_n, i, oid; int64_t err, msc, msc_k, msc_n;
overlap_region *z; ul_ov_t *p;
uint64_t k, m, mn, q[2], buf_n, rm_n, oid; int64_t err, msc, msc_k, msc_n;
overlap_region *z; ul_ov_t *p; buf->n = 0; kv_resize(uint64_t, *buf, dp);
for (k = buf_n = rm_n = 0; k < id_n; k++) {
p = &(c_idx[id_a[k]]);
q[0] = ol[ovlp_id(*p)].w_list.a[ovlp_min_wid(*p)].x_start;
q[1] = ol[ovlp_id(*p)].w_list.a[ovlp_max_wid(*p)].x_end+1;
if(q[0]<=s && q[1]>=e) {
buf[buf_n++] = id_a[k];
kv_push(uint64_t, *buf, id_a[k]);
// buf[buf_n++] = id_a[k];
}
if(q[1] < e) rm_n++;
}
buf_n = buf->n;
assert(buf_n == dp);//not right
if(buf_n > 0) {
for (k = 0, msc = INT32_MAX, msc_k = -1, msc_n = 0; k < buf_n; k++) {
p = &(c_idx[(uint32_t)buf[k]]); z = &(ol[ovlp_id(*p)]);
p = &(c_idx[(uint32_t)buf->a[k]]); z = &(ol[ovlp_id(*p)]);
// fprintf(stderr, "+++[M::%s::utg%.6dl] wid::%u, xoff::%u, coff::%u\n", __func__,
// (int32_t)ol[ovlp_id(*p)].y_id+1, ovlp_cur_wid(*p), ovlp_cur_xoff(*p), ovlp_cur_coff(*p));
err = extract_sub_cigar_err(z, s, e, p);
fprintf(stderr, "---[M::%s::utg%.6dl] wid::%u, xoff::%u, coff::%u, err::%ld\n", __func__,
(int32_t)ol[ovlp_id(*p)].y_id+1, ovlp_cur_wid(*p), ovlp_cur_xoff(*p), ovlp_cur_coff(*p), err);
// fprintf(stderr, "---[M::%s::utg%.6dl] wid::%u, xoff::%u, coff::%u, err::%ld\n", __func__,
// (int32_t)ol[ovlp_id(*p)].y_id+1, ovlp_cur_wid(*p), ovlp_cur_xoff(*p), ovlp_cur_coff(*p), err);
assert(err >= 0);
if(err < msc) {
msc = err; msc_k = k; msc_n = 1;
} else if(err == msc) {
msc_n++;
}
buf[k] |= (((uint64_t)err)<<32);
buf->a[k] |= (((uint64_t)err)<<32);
}
if(msc_n == 1) {
p = &(c_idx[(uint32_t)buf[msc_k]]);
p = &(c_idx[(uint32_t)buf->a[msc_k]]);
z = &(ol[ovlp_id(*p)]); mn = 1;
if(msc_k != 0) {
m = buf[msc_k];
buf[msc_k] = buf[0];
buf[0] = m;
m = buf->a[msc_k];
buf->a[msc_k] = buf->a[0];
buf->a[0] = m;
}
} else {
for (k = mn = 0; k < buf_n && (int64_t)mn < msc_n; k++) {
p = &(c_idx[(uint32_t)buf[k]]);
p = &(c_idx[(uint32_t)buf->a[k]]);
z = &(ol[ovlp_id(*p)]);
if((buf[k]>>32) == (uint64_t)msc) {
if((buf->a[k]>>32) == (uint64_t)msc) {
if(mn != k) {
m = buf[k];
buf[k] = buf[mn];
buf[mn] = m;
m = buf->a[k];
buf->a[k] = buf->a[mn];
buf->a[mn] = m;
}
mn++;
}
@@ -15393,56 +15436,26 @@ uint64_t gen_region_phase(overlap_region* ol, uint64_t *id_a, uint64_t id_n, uin
}
// fprintf(stderr, "[M::%s] buf_n::%ld, msc_n::%ld, mn::%lu\n", __func__, buf_n, msc_n, mn);
for (k = 0; k < buf_n; k++) {
oid = ovlp_id((c_idx[(uint32_t)buf[k]]));
buf[k] >>= 32; buf[k] <<= 32; buf[k] |= oid;
// if(k < mn) fprintf(stderr, "d::bst::[M::%s::utg%.6dl]\n", __func__, (int32_t)ol[buf[k]].y_id+1);
oid = ovlp_id((c_idx[(uint32_t)buf->a[k]]));
buf->a[k] >>= 32; buf->a[k] <<= 32; buf->a[k] |= oid;
ol[oid].overlapLen = k;
// if(s == 158482) fprintf(stderr, "k->%ld::oid->%ld[M::%s::utg%.6dl] pos::[%lu, %lu)\n", k, oid, __func__,
// (int32_t)ol[oid].y_id+1, s, e);
}
for (k = 0; k < mn; k++) {
if(buf[k]&id_set) continue;
for (i = 0; i < k; i++) {
if(query_gen_gov_idx(ovidx, id_get(buf[k]), id_get(buf[i]))) break;
}
if(i < k) {
if(!(buf[k]&id_set)) {
ol[id_get(buf[k])].overlapLen -= e - s;
ol[id_get(buf[k])].align_length -= e - s;
}
buf[k] |= id_set;
if(!(buf[i]&id_set)) {
ol[id_get(buf[i])].overlapLen -= e - s;
ol[id_get(buf[i])].align_length -= e - s;
}
buf[i] |= id_set;
}
z = &(ol[id_get(buf->a[k])]);
reassign_sec_err(ol, ovidx, buf, k);
push_sec_aln(z, s, e, 0);
}
for (k = mn; k < buf_n; k++) {
z = &(ol[id_get(buf[k])]);
z->align_length -= e - s;
for (i = 0; i < mn; i++) {
if(query_gen_gov_idx(ovidx, id_get(buf[k]), id_get(buf[i]))) break;
}
if(i < mn) {
z->align_length += e - s;
if(!(buf[k]&id_set)) {
ol[id_get(buf[k])].overlapLen -= e - s;
ol[id_get(buf[k])].align_length -= e - s;
}
buf[k] |= id_set;
if(!(buf[i]&id_set)) {
ol[id_get(buf[i])].overlapLen -= e - s;
ol[id_get(buf[i])].align_length -= e - s;
}
buf[i] |= id_set;
// fprintf(stderr, "i::bst::[M::%s::utg%.6dl]\n", __func__, (int32_t)ol[buf[k]].y_id+1);
} else {
assert(err_get(buf[i]) > (uint64_t)msc);
z->non_homopolymer_errors += err_get(buf[i])-msc;
}
z = &(ol[id_get(buf->a[k])]);
push_sec_aln(z, s, e, ((buf->a[k]&id_set)?(0):(err_get(buf->a[k])-msc)));
}
for (k = 0; k < buf_n; k++) {
ol[id_get(buf->a[k])].overlapLen = (uint32_t)-1;
}
}
@@ -15611,7 +15624,7 @@ void gen_gov_idx(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t
kv_resize(uint64_t, *idx, (uint64_t)on); memset(idx->a, 0, sizeof(*(idx->a))*on);
for (k = 0, idx->n = on; k < on; k++) {
convert_ul_ov_t(&p, &(ol->list[k]), uref); p.qn = k;
idx->a[k] = idx->n; idx->a[k] <<= 32;
// idx->a[k] = idx->n; idx->a[k] <<= 32;
for (i = on - 1; i >= 0 && i > k && ol->list[i].x_pos_e >= ol->list[k].x_pos_s; i--) {
// if(k >= i) continue;
convert_ul_ov_t(&q, &(ol->list[i]), uref); q.qn = i;
@@ -15625,23 +15638,33 @@ void gen_gov_idx(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t
if(lj->qs <= li->qs+G_CHAIN_INDEL) {
if(govlp_check(uref, uopt, bw, diff_ec_ul, li, lj)) {
idx->a[k]++; kv_push(uint64_t, *idx, i);
idx->a[k]++; idx->a[i]++;
kv_push(uint64_t, *idx, (((uint64_t)k)<<32)|((uint64_t)i));
kv_push(uint64_t, *idx, (((uint64_t)i)<<32)|((uint64_t)k));
}
} else if((lj->qe+G_CHAIN_INDEL>=li->qe) && (lj->qs+G_CHAIN_INDEL>=li->qs)) {
if(govlp_check(uref, uopt, bw, diff_ec_ul, lj, li)) {
idx->a[k]++; kv_push(uint64_t, *idx, i);
idx->a[k]++; idx->a[i]++;
kv_push(uint64_t, *idx, (((uint64_t)k)<<32)|((uint64_t)i));
kv_push(uint64_t, *idx, (((uint64_t)i)<<32)|((uint64_t)k));
}
}
}
}
radix_sort_bc64(idx->a + on, idx->a + idx->n);
for (k = 0, os = oe = on; k < on; k++) {
oe = os + idx->a[k];
idx->a[k] = (os<<32)|oe;
os = oe;
}
// for (k = 0; k < on; k++) {
// int64_t s, e;
// s = idx->a[k]>>32; e = s + (uint32_t)idx->a[k];
// s = idx->a[k]>>32; e = (uint32_t)idx->a[k];
// for (i = s; i < e; i++) {
// assert((idx->a[i]>>32) == (uint32_t)k);
// fprintf(stderr, "k::%ld[M::%s::utg%.6dl] utg%.6dl\n", k, __func__,
// (int32_t)ol->list[k].y_id+1, (int32_t)ol->list[idx->a[i]].y_id+1);
// (int32_t)ol->list[k].y_id+1, (int32_t)ol->list[(uint32_t)idx->a[i]].y_id+1);
// }
// }
}
@@ -15663,6 +15686,19 @@ void prt_overlap_region_stat(overlap_region *z)
}
void prt_overlap_region_phase_stat(overlap_region *z)
{
uint64_t k = 0;
fprintf(stderr, "[M::%s::utg%.6dl::%c] q::[%d, %d), t::[%d, %d), best::%u, sec::%u\n", __func__,
(int32_t)z->y_id+1, "+-"[z->y_pos_strand], z->x_pos_s, z->x_pos_e+1, z->y_pos_s, z->y_pos_e+1,
z->align_length, z->non_homopolymer_errors);
for (k = 0; k < z->w_list.n; k++) {
fprintf(stderr, "[k::%lu] q::[%d, %d), sec::%u\n", k,
z->w_list.a[k].x_start, z->w_list.a[k].x_end, z->w_list.a[k].clen);
}
}
void region_phase(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t *uopt, kv_ul_ov_t *c_idx, asg64_v* idx, asg64_v* buf, asg64_v* buf1)
{
int64_t on = ol->length, k, i, zwn, q[2], t[2], w[2];
@@ -15671,7 +15707,9 @@ void region_phase(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t
kv_resize(ul_ov_t, *c_idx, ol->length);
for (k = idx->n = c_idx->n = 0; k < on; k++) {
z = &(ol->list[k]); zwn = z->w_list.n;
z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s; z->non_homopolymer_errors = 0;
// z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s;
z->align_length = 0; z->overlapLen = (uint32_t)-1;
z->non_homopolymer_errors = 0;
if(!zwn) continue;
q[0] = q[1] = t[0] = t[1] = w[0] = w[1] = INT32_MIN;
for (i = 0; i < zwn; i++) {
@@ -15716,17 +15754,16 @@ void region_phase(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t
}
}
radix_sort_bc64(idx->a, idx->a+idx->n);
kv_resize(uint64_t, *buf, idx->n);
gen_gov_idx(ol, uref, uopt, G_CHAIN_BW, N_GCHAIN_RATE, buf1);
for (m = 0; m < c_idx->n; m++) {
fprintf(stderr, "+++[M::%s::utg%.6dl] q[%d, %d), t[%d, %d), wn::%d\n", __func__,
(int32_t)ol->list[ovlp_id(c_idx->a[m])].y_id+1,
ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_min_wid(c_idx->a[m])].x_start,
ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_max_wid(c_idx->a[m])].x_end+1,
ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_min_wid(c_idx->a[m])].y_start,
ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_max_wid(c_idx->a[m])].y_end+1,
ovlp_max_wid(c_idx->a[m])+1-ovlp_min_wid(c_idx->a[m]));
}
// for (m = 0; m < c_idx->n; m++) {
// fprintf(stderr, "+++[M::%s::utg%.6dl] q[%d, %d), t[%d, %d), wn::%d\n", __func__,
// (int32_t)ol->list[ovlp_id(c_idx->a[m])].y_id+1,
// ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_min_wid(c_idx->a[m])].x_start,
// ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_max_wid(c_idx->a[m])].x_end+1,
// ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_min_wid(c_idx->a[m])].y_start,
// ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_max_wid(c_idx->a[m])].y_end+1,
// ovlp_max_wid(c_idx->a[m])+1-ovlp_min_wid(c_idx->a[m]));
// }
int64_t srt_n = idx->n, dp, old_dp, beg, end;
@@ -15742,15 +15779,31 @@ void region_phase(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t
}
// fprintf(stderr, "\n[M::%s::] beg::%ld, end::%ld, old_dp::%ld\n", __func__, beg, end, old_dp);
if((end > beg) && (old_dp >= 2)) {
fprintf(stderr, "\n[M::%s::] beg::%ld, end::%ld, old_dp::%ld\n", __func__, beg, end, old_dp);
idx->n = srt_n + gen_region_phase(ol->list, idx->a+srt_n, idx->n-srt_n, beg, end, old_dp, c_idx->a, buf->a, buf1);
// fprintf(stderr, "\n[M::%s::] beg::%ld, end::%ld, old_dp::%ld\n", __func__, beg, end, old_dp);
// kv_resize(uint64_t, *buf, ((uint32_t)old_dp)<<1);
idx->n = srt_n + gen_region_phase(ol->list, idx->a+srt_n, idx->n-srt_n, beg, end, old_dp, c_idx->a, buf, buf1);
}
beg = end;
}
///hap->length
for (k = 0; k < on; k++) {
prt_overlap_region_stat(&(ol->list[k]));
z = &(ol->list[k]);
z->overlapLen = z->x_pos_e+1-z->x_pos_s;
z->non_homopolymer_errors = 0; zwn = 0;
for (i = m = 0; i < z->align_length; i++) {
z->w_list.a[m] = z->w_list.a[z->w_list.n+i];
if(z->w_list.a[m].clen > 0) {
z->non_homopolymer_errors += z->w_list.a[m].clen;
zwn += z->w_list.a[m].x_end-z->w_list.a[m].x_start;
}
m++;
}
z->w_list.n = m; assert(zwn <= z->overlapLen);
z->align_length = z->overlapLen - zwn;
// fprintf(stderr, "[M::%s::utg%.6dl::%c] all::%u, non-best::%ld, best::%u\n", __func__,
// (int32_t)z->y_id+1, "+-"[z->y_pos_strand], z->overlapLen, zwn, z->align_length);
// prt_overlap_region_phase_stat(&(ol->list[k]));
// z = &(ol->list[k]);
// if(z->align_length == z->overlapLen) {///prefer alignments without any trans hit
// z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s;