fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-05 03:38:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

r1256: working for one example, but still buggy

Browse Source
This commit is contained in:
Heng Li
2025-04-06 10:33:57 -04:00
parent 1877818239
commit a8094ad859
6 changed files with 37 additions and 13 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+8 -1
View File
@@ -82,6 +82,7 @@ static ko_longopt_t long_options[] = {
{ "spsc", ko_required_argument, 357 },
{ "junc-pen", ko_required_argument, 358 },
{ "pe-ind-chain", ko_no_argument, 359 },
{ "jump-bed", ko_required_argument, 360 },
{ "dbg-seed-occ", ko_no_argument, 501 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
@@ -131,7 +132,7 @@ int main(int argc, char *argv[])
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, n_parts, old_best_n = -1;
char *fnw = 0, *rg = 0, *junc_bed = 0, *fn_spsc = 0, *s, *alt_list = 0;
char *fnw = 0, *rg = 0, *junc_bed = 0, *jump_bed = 0, *fn_spsc = 0, *s, *alt_list = 0;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
mm_idx_t *mi;
@@ -254,6 +255,7 @@ 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 == 359) opt.flag |= MM_F_PE_IND; // --pe-ind-chain
else if (c == 360) jump_bed = o.arg; // --jump-bed
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");
@@ -440,6 +442,11 @@ int main(int argc, char *argv[])
if (mi->I == 0 && mm_verbose >= 2)
fprintf(stderr, "[WARNING] failed to load the junction BED file\n");
}
if (jump_bed) {
mm_idx_bed_read2(mi, jump_bed, 1, 0, 1);
if (mi->J == 0 && mm_verbose >= 2)
fprintf(stderr, "[WARNING] failed to load the jump BED file\n");
}
if (fn_spsc) {
mm_idx_spsc_read(mi, fn_spsc, mm_max_spsc_bonus(&opt));
if (mi->spsc == 0 && mm_verbose >= 2)