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lh3lh3
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r1248: support --end-bonus in splice mode
but this is not enabled by default for now
1 parent 924fc4d commit 9d06cef

6 files changed

Lines changed: 20 additions & 16 deletions

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‎align.c‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -330,7 +330,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
330330
{
331331
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
332332
int i;
333-
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);
333+
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);
334334
for (i = 0; i < tlen; ++i) fputc("ACGTN"[tseq[i]], stderr);
335335
fputc('\n', stderr);
336336
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
344344
} else if (opt->flag & MM_F_SPLICE) { // spliced alignment
345345
assert((ksw_flag & KSW_EZ_SPLICE_FOR) == 0 || (ksw_flag & KSW_EZ_SPLICE_REV) == 0);
346346
if (!(opt->flag & MM_F_SPLICE_OLD)) ksw_flag |= KSW_EZ_SPLICE_CMPLX;
347-
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);
347+
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);
348348
} else if (opt->q == opt->q2 && opt->e == opt->e2) { // affine gap
349349
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, ksw_flag, ez);
350350
} else { // dual affine gap

‎ksw2.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -72,7 +72,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
7272
int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
7373

7474
void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
75-
int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
75+
int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
7676

7777
void ksw_extf2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez);
7878

‎ksw2_dispatch.c‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -80,17 +80,17 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
8080
}
8181

8282
void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
83-
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
83+
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
8484
{
8585
extern void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
86-
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
86+
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
8787
extern void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
88-
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
88+
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
8989
if (ksw_simd < 0) ksw_simd = x86_simd();
9090
if (ksw_simd & SIMD_SSE4_1)
91-
ksw_exts2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, junc_bonus, junc_pen, flag, junc, ez);
91+
ksw_exts2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, end_bonus, junc_bonus, junc_pen, flag, junc, ez);
9292
else if (ksw_simd & SIMD_SSE2)
93-
ksw_exts2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, junc_bonus, junc_pen, flag, junc, ez);
93+
ksw_exts2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, end_bonus, junc_bonus, junc_pen, flag, junc, ez);
9494
else abort();
9595
}
9696
#endif

‎ksw2_exts2_sse.c‎

Lines changed: 9 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -24,14 +24,14 @@
2424
#ifdef KSW_CPU_DISPATCH
2525
#ifdef __SSE4_1__
2626
void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
27-
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
27+
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
2828
#else
2929
void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
30-
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
30+
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
3131
#endif
3232
#else
3333
void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
34-
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
34+
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
3535
#endif // ~KSW_CPU_DISPATCH
3636
{
3737
#define __dp_code_block1 \
@@ -452,10 +452,14 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
452452
if (!approx_max) kfree(km, H);
453453
if (with_cigar) { // backtrack
454454
int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
455-
if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY))
455+
if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY)) {
456456
ksw_backtrack(km, 1, rev_cigar, long_thres, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
457-
else if (ez->max_t >= 0 && ez->max_q >= 0)
457+
} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > (int)ez->max) {
458+
ez->reach_end = 1;
459+
ksw_backtrack(km, 1, rev_cigar, long_thres, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
460+
} else if (ez->max_t >= 0 && ez->max_q >= 0) {
458461
ksw_backtrack(km, 1, rev_cigar, long_thres, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
462+
}
459463
kfree(km, mem2); kfree(km, off);
460464
}
461465
}

‎minimap.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
#include <stdio.h>
66
#include <sys/types.h>
77

8-
#define MM_VERSION "2.28-r1245-dirty"
8+
#define MM_VERSION "2.28-r1248-dirty"
99

1010
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
1111
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name

‎minimap2.1‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
.TH minimap2 1 "30 March 2025" "minimap2-2.28-dirty (r1237)" "Bioinformatics tools"
1+
.TH minimap2 1 "2 April 2025" "minimap2-2.28-dirty (r1248)" "Bioinformatics tools"
22
.SH NAME
33
.PP
44
minimap2 - mapping and alignment between collections of DNA sequences
@@ -689,7 +689,7 @@ Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq
689689
.B splice:sr
690690
Spliced alignment for short RNA-seq reads
691691
.RB ( -xsplice:hq
692-
.B --frag=yes --end-bonus=10 -2K50m --heap-sort=yes --pe-ind-chain
692+
.B --frag=yes -m25 -s40 -2K50m --heap-sort=yes --pe-ind-chain
693693
.BR --secondary=no ).
694694
.TP
695695
.B sr

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