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r1248: support --end-bonus in splice mode

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but this is not enabled by default for now
This commit is contained in:
Heng Li
2025-04-02 21:39:41 -04:00
parent 924fc4d671
commit 9d06cef13e
6 changed files with 20 additions and 16 deletions
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align.c
+2 -2
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@@ -330,7 +330,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
{
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
int i;
fprintf(stderr, "===> q=(%d,%d), e=(%d,%d), bw=%d, ksw_flag=%d, zdrop=%d <===\n", opt->q, opt->q2, opt->e, opt->e2, w, ksw_flag, opt->zdrop);
fprintf(stderr, "===> q=(%d,%d), e=(%d,%d), bw=%d, ksw_flag=%d, zdrop=%d, end_bonus=%d <===\n", opt->q, opt->q2, opt->e, opt->e2, w, ksw_flag, opt->zdrop, end_bonus);
for (i = 0; i < tlen; ++i) fputc("ACGTN"[tseq[i]], stderr);
fputc('\n', stderr);
for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr);
@@ -344,7 +344,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
} else if (opt->flag & MM_F_SPLICE) { // spliced alignment
assert((ksw_flag & KSW_EZ_SPLICE_FOR) == 0 || (ksw_flag & KSW_EZ_SPLICE_REV) == 0);
if (!(opt->flag & MM_F_SPLICE_OLD)) ksw_flag |= 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, opt->junc_pen, ksw_flag, junc, ez);
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, end_bonus, opt->junc_bonus, opt->junc_pen, ksw_flag, junc, ez);
} else if (opt->q == opt->q2 && opt->e == opt->e2) { // affine gap
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, ksw_flag, ez);
} else { // dual affine gap