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r1164: changed the syntax of -J
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@lh3
lh3 committed Apr 8, 2023
1 parent a026c69 commit 5e72423
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Showing 3 changed files with 43 additions and 39 deletions.
2 changes: 1 addition & 1 deletion align.c
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Original file line number Diff line number Diff line change
Expand Up @@ -328,7 +328,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
ez->zdropped = 1;
} else if (opt->flag & MM_F_SPLICE) {
int flag_tmp = flag;
if (opt->flag & MM_F_SPLICE_CMPLX) flag_tmp |= KSW_EZ_SPLICE_CMPLX;
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);
} 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);
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12 changes: 8 additions & 4 deletions main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,6 @@ static ko_longopt_t long_options[] = {
{ "min-dp-len", ko_required_argument, 308 },
{ "print-aln-seq", ko_no_argument, 309 },
{ "splice", ko_no_argument, 310 },
{ "splice-model", ko_no_argument, 'J' },
{ "cost-non-gt-ag", ko_required_argument, 'C' },
{ "no-long-join", ko_no_argument, 312 },
{ "sr", ko_no_argument, 313 },
Expand Down Expand Up @@ -120,7 +119,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int64_t flag, int long_idx, const

int main(int argc, char *argv[])
{
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:e:U:j:J";
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:e:U:j:J:";
ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt;
mm_idxopt_t ipt;
Expand Down Expand Up @@ -187,8 +186,12 @@ int main(int argc, char *argv[])
else if (c == 'R') rg = o.arg;
else if (c == 'h') fp_help = stdout;
else if (c == '2') opt.flag |= MM_F_2_IO_THREADS;
else if (c == 'J') opt.flag |= MM_F_SPLICE_CMPLX; // --splice-model
else if (c == 'o') {
else if (c == 'J') {
int t;
t = atoi(o.arg);
if (t == 0) opt.flag |= MM_F_SPLICE_OLD;
else if (t == 1) opt.flag &= ~MM_F_SPLICE_OLD;
} else if (c == 'o') {
if (strcmp(o.arg, "-") != 0) {
if (freopen(o.arg, "wb", stdout) == NULL) {
fprintf(stderr, "[ERROR]\033[1;31m failed to write the output to file '%s'\033[0m: %s\n", o.arg, strerror(errno));
Expand Down Expand Up @@ -347,6 +350,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -z INT[,INT] Z-drop score and inversion Z-drop score [%d,%d]\n", opt.zdrop, opt.zdrop_inv);
fprintf(fp_help, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
fprintf(fp_help, " -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
fprintf(fp_help, " -J INT splice mode. 0: original minimap2 model; 1: miniprot model [1]\n");
fprintf(fp_help, " Input/Output:\n");
fprintf(fp_help, " -a output in the SAM format (PAF by default)\n");
fprintf(fp_help, " -o FILE output alignments to FILE [stdout]\n");
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68 changes: 34 additions & 34 deletions minimap.h
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Original file line number Diff line number Diff line change
Expand Up @@ -5,44 +5,44 @@
#include <stdio.h>
#include <sys/types.h>

#define MM_VERSION "2.24-r1163-dirty"

#define MM_F_NO_DIAG 0x001 // no exact diagonal hit
#define MM_F_NO_DUAL 0x002 // skip pairs where query name is lexicographically larger than target name
#define MM_F_CIGAR 0x004
#define MM_F_OUT_SAM 0x008
#define MM_F_NO_QUAL 0x010
#define MM_F_OUT_CG 0x020
#define MM_F_OUT_CS 0x040
#define MM_F_SPLICE 0x080 // splice mode
#define MM_F_SPLICE_FOR 0x100 // match GT-AG
#define MM_F_SPLICE_REV 0x200 // match CT-AC, the reverse complement of GT-AG
#define MM_F_NO_LJOIN 0x400
#define MM_F_OUT_CS_LONG 0x800
#define MM_F_SR 0x1000
#define MM_F_FRAG_MODE 0x2000
#define MM_F_NO_PRINT_2ND 0x4000
#define MM_F_2_IO_THREADS 0x8000
#define MM_F_LONG_CIGAR 0x10000
#define MM_F_INDEPEND_SEG 0x20000
#define MM_F_SPLICE_FLANK 0x40000
#define MM_F_SOFTCLIP 0x80000
#define MM_F_FOR_ONLY 0x100000
#define MM_F_REV_ONLY 0x200000
#define MM_F_HEAP_SORT 0x400000
#define MM_F_ALL_CHAINS 0x800000
#define MM_F_OUT_MD 0x1000000
#define MM_F_COPY_COMMENT 0x2000000
#define MM_F_EQX 0x4000000 // use =/X instead of M
#define MM_F_PAF_NO_HIT 0x8000000 // output unmapped reads to PAF
#define MM_F_NO_END_FLT 0x10000000
#define MM_F_HARD_MLEVEL 0x20000000
#define MM_F_SAM_HIT_ONLY 0x40000000
#define MM_VERSION "2.24-r1164-dirty"

#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name
#define MM_F_CIGAR (0x004LL)
#define MM_F_OUT_SAM (0x008LL)
#define MM_F_NO_QUAL (0x010LL)
#define MM_F_OUT_CG (0x020LL)
#define MM_F_OUT_CS (0x040LL)
#define MM_F_SPLICE (0x080LL) // splice mode
#define MM_F_SPLICE_FOR (0x100LL) // match GT-AG
#define MM_F_SPLICE_REV (0x200LL) // match CT-AC, the reverse complement of GT-AG
#define MM_F_NO_LJOIN (0x400LL)
#define MM_F_OUT_CS_LONG (0x800LL)
#define MM_F_SR (0x1000LL)
#define MM_F_FRAG_MODE (0x2000LL)
#define MM_F_NO_PRINT_2ND (0x4000LL)
#define MM_F_2_IO_THREADS (0x8000LL)
#define MM_F_LONG_CIGAR (0x10000LL)
#define MM_F_INDEPEND_SEG (0x20000LL)
#define MM_F_SPLICE_FLANK (0x40000LL)
#define MM_F_SOFTCLIP (0x80000LL)
#define MM_F_FOR_ONLY (0x100000LL)
#define MM_F_REV_ONLY (0x200000LL)
#define MM_F_HEAP_SORT (0x400000LL)
#define MM_F_ALL_CHAINS (0x800000LL)
#define MM_F_OUT_MD (0x1000000LL)
#define MM_F_COPY_COMMENT (0x2000000LL)
#define MM_F_EQX (0x4000000LL) // use =/X instead of M
#define MM_F_PAF_NO_HIT (0x8000000LL) // output unmapped reads to PAF
#define MM_F_NO_END_FLT (0x10000000LL)
#define MM_F_HARD_MLEVEL (0x20000000LL)
#define MM_F_SAM_HIT_ONLY (0x40000000LL)
#define MM_F_RMQ (0x80000000LL)
#define MM_F_QSTRAND (0x100000000LL)
#define MM_F_NO_INV (0x200000000LL)
#define MM_F_NO_HASH_NAME (0x400000000LL)
#define MM_F_SPLICE_CMPLX (0x800000000LL)
#define MM_F_SPLICE_OLD (0x800000000LL)

#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2
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