fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-15 13:07:55 +08:00
Code Issues Packages Projects Releases Wiki Activity

r1272: support pass-1 junction processing

Browse Source 
NOT tested yet
This commit is contained in:
Heng Li
2025-04-12 23:15:04 -04:00
parent d930ea94ad
commit fb81e150f2
4 changed files with 125 additions and 59 deletions
Download Patch File Download Diff File Expand all files Collapse all files

21
main.c
View File

@@ -84,6 +84,7 @@ static ko_longopt_t long_options[] = {
{ "pairing", ko_required_argument, 359 },
{ "jump-min-match", ko_required_argument, 360 },
{ "write-junc", ko_no_argument, 361 },
{ "jump-pass1", ko_required_argument, 362 },
{ "dbg-seed-occ", ko_no_argument, 501 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
@@ -133,7 +134,7 @@ 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, *jump_bed = 0, *fn_spsc = 0, *s, *alt_list = 0;
char *fnw = 0, *rg = 0, *fn_bed_junc = 0, *fn_bed_jump = 0, *fn_bed_pass1 = 0, *fn_spsc = 0, *s, *alt_list = 0;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
mm_idx_t *mi;
@@ -195,7 +196,7 @@ 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') jump_bed = o.arg;
else if (c == 'j') fn_bed_jump = o.arg;
else if (c == 'J') {
int t;
t = atoi(o.arg);
@@ -237,7 +238,7 @@ int main(int argc, char *argv[])
else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
else if (c == 340) junc_bed = o.arg; // --junc-bed
else if (c == 340) fn_bed_junc = o.arg; // --junc-bed
else if (c == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
else if (c == 358) opt.junc_pen = atoi(o.arg); // --junc-pen
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
@@ -257,6 +258,7 @@ int main(int argc, char *argv[])
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 == 362) fn_bed_pass1 = o.arg; // --jump-pass1
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");
@@ -458,16 +460,21 @@ int main(int argc, char *argv[])
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
if (mm_verbose >= 3) mm_idx_stat(mi);
if (junc_bed) {
mm_idx_bed_read(mi, junc_bed, 1);
if (fn_bed_junc) {
mm_idx_bed_read(mi, fn_bed_junc, 1);
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 (fn_bed_jump) {
mm_idx_jjump_read(mi, fn_bed_jump, MM_JUNC_ANNO, -1);
if (mi->J == 0 && mm_verbose >= 2)
fprintf(stderr, "[WARNING] failed to load the jump BED file\n");
}
if (fn_bed_pass1) {
mm_idx_jjump_read(mi, fn_bed_pass1, MM_JUNC_MISC, 5);
if (mi->J == 0 && mm_verbose >= 2)
fprintf(stderr, "[WARNING] failed to load the pass-1 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)