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cuttoff before debugging

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chhylp123
2022-11-05 09:03:23 -04:00
parent e66c003b65
commit 612c1ab712
8 changed files with 1115 additions and 93 deletions
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Correct.cpp
+80
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@@ -15213,6 +15213,75 @@ UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql,
#define ovlp_cur_xoff(x) ((x).qs)
#define ovlp_cur_coff(x) ((x).qe)
int64_t retrieve_cigar_err_debug(bit_extz_t *ez, int64_t s, int64_t e)
{
if(!ez->cigar.n) return 0;
int64_t err = 0, xk = ez->ts; int64_t ws, we, os, oe, ovlp;
uint32_t ck = 0, cl; uint16_t op;
os = MAX(s, ez->ts); oe = MIN(e, ez->te+1);
ovlp = ((oe>os)? (oe-os):0);
if(!ovlp) {
fprintf(stderr, "[M::%s::] s::%ld, e::%ld, ez->ts::%u, ez->te::%u\n",
__func__, s, e, ez->ts, ez->te);
}
assert(ovlp);
//some cigar will span s or e
while (ck < ez->cigar.n && xk < e) {//[s, e)
ws = xk;
ck = pop_trace(&(ez->cigar), ck, &op, &cl);
if(op!=2) xk += cl;
we = xk;
os = MAX(s, ws); oe = MIN(e, we);
ovlp = ((oe>os)? (oe-os):0);
if((op==2) && (ws>=s) && (ws<e)) {
ovlp = cl;
}
if((!ovlp) || (!op)) continue;
err += ovlp;
}
return err;
}
///[s, e)
int64_t extract_sub_cigar_err_debug(overlap_region *z, int64_t s, int64_t e)
{
int64_t wk = 0, wn = z->w_list.n, ws, we, os, oe, ovlp;
window_list *m; int64_t xl, yl, werr, err; bit_extz_t ez;
for (wk = err = 0; wk < wn; wk++) {
m = &(z->w_list.a[wk]);
ws = m->x_start; we = m->x_end+1;
if(ws >= e) break;
os = MAX(s, ws); oe = MIN(e, we);
ovlp = ((oe>os)? (oe-os):0);
if(ovlp) {
xl = m->x_end+1-m->x_start;
yl = m->y_end+1-m->y_start;
if((is_ualn_win((*m))) || (is_est_aln((*m)))) {
if(is_ualn_win((*m))) { //unmapped
werr = gen_err_unaligned(xl, yl);
} else {
werr = m->error;//shared window
}
if(ovlp < xl) {
werr = (((double)ovlp)/((double)xl))*((double)werr);
}
//skip the whole window
err += werr;
} else {
if(ovlp == xl) {
//skip the whole window
err += m->error;
} else {
set_bit_extz_t(ez, (*z), wk);
err += retrieve_cigar_err_debug(&ez, os, oe);
}
}
}
}
return err;
}
int64_t retrieve_cigar_err(bit_extz_t *ez, int64_t s, int64_t e, int64_t *xk, int64_t *ck)
{
@@ -15243,6 +15312,13 @@ int64_t retrieve_cigar_err(bit_extz_t *ez, int64_t s, int64_t e, int64_t *xk, in
if((!ovlp) || (!op)) continue;
err += ovlp;
}
// int64_t debug_err = retrieve_cigar_err_debug(ez, s, e);
// if(!(err == debug_err)) {
// fprintf(stderr, "[M::%s::] err::%ld, debug_err::%ld, s::%ld, e::%ld, ez->ts::%u, ez->te::%u\n",
// __func__, err, debug_err, s, e, ez->ts, ez->te);
// }
// assert(err == debug_err);
return err;
}
///[s, e)
@@ -15401,6 +15477,10 @@ uint64_t gen_region_phase(overlap_region* ol, uint64_t *id_a, uint64_t id_n, uin
// 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);
// int64_t debug_err = extract_sub_cigar_err_debug(z, s, e);
// assert(err == debug_err);
// fprintf(stderr, "[M::%s::] err::%ld, debug_err::%ld\n", __func__, err, debug_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);