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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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8
align.c
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@@ -326,9 +326,11 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
if (opt->max_sw_mat > 0 && (int64_t)tlen * qlen > opt->max_sw_mat) {
ksw_reset_extz(ez);
ez->zdropped = 1;
} else if (opt->flag & MM_F_SPLICE)
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, flag, junc, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2)
} else if (opt->flag & MM_F_SPLICE) {
int flag_tmp = flag;
if (opt->flag & MM_F_SPLICE_CMPLX) flag_tmp |= KSW_EZ_SPLICE_CMPLX;
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, flag_tmp, junc, ez);
} else if (opt->q == opt->q2 && opt->e == opt->e2)
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, flag, ez);
else
ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);