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added --junc-pen; it does nothing for now

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Heng Li
2024-10-11 21:27:25 -04:00
parent e4e1f7843b
commit 042c8d4d71
7 changed files with 15 additions and 11 deletions
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align.c
+1 -1
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@@ -343,7 +343,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
} else if (opt->flag & MM_F_SPLICE) {
int flag_tmp = flag;
if (!(opt->flag & MM_F_SPLICE_OLD)) 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);
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, opt->junc_pen, 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