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fill the junction array

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modifying ksw will be the next
This commit is contained in:
Heng Li
2024-10-11 23:22:23 -04:00
parent 042c8d4d71
commit 8efe83b744
3 changed files with 40 additions and 25 deletions
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ksw2_exts2_sse.c
+5 -1
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@@ -191,7 +191,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
}
}
if (junc) {
if (junc && !(flag & KSW_EZ_SPLICE_SCORE)) {
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)))
@@ -207,6 +207,10 @@ 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) {