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miniprot-like splice model

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slightly worse on iso-seq and slightly better on direct-RNA
This commit is contained in:
Heng Li
2022-10-06 09:10:17 -04:00
parent 5aa4355ca8
commit 6c2cbf7903
7 changed files with 104 additions and 7 deletions
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ksw2_exts2_sse.c
+90 -1
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@@ -62,6 +62,8 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
b = _mm_sub_epi8(b, tmp); \
a2= _mm_sub_epi8(a2, _mm_sub_epi8(z, q2_));
const int sp[4] = { 4, 7, 10, 15 };
// const int sp[4] = { 3, 5, 7, 10 };
int r, t, qe = q + e, n_col_, *off = 0, *off_end = 0, tlen_, qlen_, last_st, last_en, max_sc, min_sc, long_thres, long_diff;
int with_cigar = !(flag&KSW_EZ_SCORE_ONLY), approx_max = !!(flag&KSW_EZ_APPROX_MAX);
int32_t *H = 0, H0 = 0, last_H0_t = 0;
@@ -71,6 +73,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
ksw_reset_extz(ez);
if (m <= 1 || qlen <= 0 || tlen <= 0 || q2 <= q + e) return;
assert((flag & KSW_EZ_SPLICE_FOR) == 0 || (flag & KSW_EZ_SPLICE_REV) == 0); // can't be both set
zero_ = _mm_set1_epi8(0);
q_ = _mm_set1_epi8(q);
@@ -117,7 +120,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
memcpy(sf, target, tlen);
// set the donor and acceptor arrays. TODO: this assumes 0/1/2/3 encoding!
if (flag & (KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV)) {
if ((flag & (KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV)) && !(flag & KSW_EZ_SPLICE_CMPLX)) {
int semi_cost = flag&KSW_EZ_SPLICE_FLANK? -noncan/2 : 0; // GTr or yAG is worth 0.5 bit; see PMID:18688272
memset(donor, -noncan, tlen_ * 16);
memset(acceptor, -noncan, tlen_ * 16);
@@ -168,6 +171,92 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&8)))
((int8_t*)acceptor)[t] += junc_bonus;
}
} else if (flag & (KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV)) {
memset(donor, -sp[3], tlen_ * 16);
memset(acceptor, -sp[3], tlen_ * 16);
if (!(flag & KSW_EZ_REV_CIGAR)) {
for (t = 0; t < tlen - 4; ++t) {
int x = 3, y = 3, z;
if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t+1] == 2 && target[t+2] == 3) // GT.
x = target[t+3] == 0 || target[t+3] == 2? -1 : 0;
else if (target[t+1] == 2 && target[t+2] == 1) x = 1; // GC.
else if (target[t+1] == 0 && target[t+2] == 3) x = 2; // AT.
}
if (flag & KSW_EZ_SPLICE_REV) {
if (target[t+1] == 1 && target[t+2] == 3) // CT. (revcomp of .AG)
y = target[t+3] == 0 || target[t+3] == 2? -1 : 0;
else if (target[t+1] == 2 && target[t+2] == 3) y = 2; // GT. (revcomp of .AC)
}
z = x < y? x : y;
((int8_t*)donor)[t] = z < 0? 0 : -sp[z];
}
if (junc)
for (t = 0; t < tlen - 1; ++t)
if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&8)))
((int8_t*)donor)[t] += junc_bonus;
for (t = 2; t < tlen; ++t) {
int x = 3, y = 3, z;
if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t-1] == 0 && target[t] == 2) // .AG
x = target[t-2] == 1 || target[t-2] == 3? -1 : 0;
else if (target[t-1] == 0 && target[t] == 1) x = 2; // .AC
}
if (flag & KSW_EZ_SPLICE_REV) {
if (target[t-1] == 0 && target[t] == 1) // .AC (revcomp of GT.)
y = target[t-2] == 1 || target[t-2] == 3? -1 : 0;
else if (target[t-1] == 1 && target[t] == 2) y = 1; // .CG
else if (target[t-1] == 0 && target[t] == 3) y = 1; // .AT
}
z = x < y? x : y;
((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
}
if (junc)
for (t = 0; t < tlen; ++t)
if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&4)))
((int8_t*)acceptor)[t] += junc_bonus;
} else {
for (t = 0; t < tlen - 4; ++t) {
int x = 3, y = 3, z;
if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t+1] == 2 && target[t+2] == 0) // GA. (rev of .AG)
x = target[t+3] == 1 || target[t+3] == 3? -1 : 0;
else if (target[t+1] == 1 && target[t+2] == 0) x = 2; // CA. (rev of .AC)
}
if (flag & KSW_EZ_SPLICE_REV) {
if (target[t+1] == 1 && target[t+2] == 0) // CA. (comp of GT.)
y = target[t+3] == 1 || target[t+3] == 3? -1 : 0;
else if (target[t+1] == 1 && target[t+2] == 2) y = 1; // CG. (comp of GC.)
else if (target[t+1] == 3 && target[t+2] == 0) y = 2; // TA. (comp of AT.)
}
z = x < y? x : y;
((int8_t*)donor)[t] = z < 0? 0 : -sp[z];
}
if (junc)
for (t = 0; t < tlen - 1; ++t)
if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&4)))
((int8_t*)donor)[t] += junc_bonus;
for (t = 2; t < tlen; ++t) {
int x = 3, y = 3, z;
if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t-1] == 3 && target[t] == 2) // .TG (rev of GT.)
x = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
else if (target[t-1] == 1 && target[t] == 2) x = 1; // .CG
else if (target[t-1] == 3 && target[t] == 0) x = 2; // .TA
}
if (flag & KSW_EZ_SPLICE_REV) {
if (target[t-1] == 3 && target[t] == 1) // .TC (comp of .AG)
y = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
else if (target[t-1] == 3 && target[t] == 2) y = 2; // .TG
}
z = x < y? x : y;
((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
}
if (junc)
for (t = 0; t < tlen; ++t)
if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&8)))
((int8_t*)acceptor)[t] += junc_bonus;
}
}
for (r = 0, last_st = last_en = -1; r < qlen + tlen - 1; ++r) {