fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-07 13:08:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r1269: added --write-junc

Browse Source 
in preparation for 2-pass
This commit is contained in:
Heng Li
2025-04-11 01:00:15 -04:00
parent bd03d975fc
commit a5411fc3c0
5 changed files with 59 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+2
View File
@@ -83,6 +83,7 @@ static ko_longopt_t long_options[] = {
{ "junc-pen", ko_required_argument, 358 },
{ "pairing", ko_required_argument, 359 },
{ "jump-min-match", ko_required_argument, 360 },
{ "write-junc", ko_no_argument, 361 },
{ "dbg-seed-occ", ko_no_argument, 501 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
@@ -255,6 +256,7 @@ int main(int argc, char *argv[])
else if (c == 356) opt.rmq_inner_dist = mm_parse_num(o.arg); // --rmq-inner
else if (c == 357) fn_spsc = o.arg; // --spsc
else if (c == 360) opt.jump_min_match = mm_parse_num(o.arg); // --jump-min-match
else if (c == 361) opt.flag |= MM_F_OUT_JUNC | MM_F_CIGAR; // --write-junc
else if (c == 501) mm_dbg_flag |= MM_DBG_SEED_FREQ; // --dbg-seed-occ
else if (c == 330) {
fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");