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implemented ksw scoring; not tested

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This commit is contained in:
Heng Li
2024-10-11 23:58:18 -04:00
parent 8efe83b744
commit d1f4c8d232
1 changed files with 7 additions and 5 deletions
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12
ksw2_exts2_sse.c
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@@ -191,7 +191,13 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
}
}
if (junc && !(flag & KSW_EZ_SPLICE_SCORE)) {
if (junc && (flag & KSW_EZ_SPLICE_SCORE)) { // junc[] keeps the donor score
uint8_t donor_val = !(flag & KSW_EZ_REV_CIGAR)? 0 : 1;
for (t = 0; t < tlen - 1; ++t)
((int8_t*)donor)[t] += junc[t+1] == 0xff? -junc_pen : (junc[t+1]&1) == donor_val? (int8_t)(junc[t+1]>>1) - (int8_t)KSW_SPSC_OFFSET : 0;
for (t = 0; t < tlen - 1; ++t)
((int8_t*)acceptor)[t] += junc[t+1] == 0xff? -junc_pen : (junc[t+1]&1) == !donor_val? (int8_t)(junc[t+1]>>1) - (int8_t)KSW_SPSC_OFFSET : 0;
} else if (junc) { // junc[] keeps the splice sites
if (!(flag & KSW_EZ_REV_CIGAR)) {
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)))
@@ -207,10 +213,6 @@ 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 (junc) {
if (!(flag & KSW_EZ_REV_CIGAR)) {
} else {
}
}
for (r = 0, last_st = last_en = -1; r < qlen + tlen - 1; ++r) {