fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-01 16:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r1164: changed the syntax of -J

Browse Source
This commit is contained in:
Heng Li
2023-04-07 22:54:33 -04:00
parent a026c69b89
commit 5e7242303c
3 changed files with 42 additions and 38 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+8 -4
View File
@@ -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 },
@@ -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;
@@ -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));
@@ -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");