fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-29 22:08:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

BED I/O

Browse Source
This commit is contained in:
Heng Li
2018-09-16 14:49:53 -04:00
parent c63a33904f
commit 2b653ecda3
5 changed files with 113 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+4 -1
View File
@@ -59,6 +59,7 @@ static ko_longopt_t long_options[] = {
{ "paf-no-hit", ko_no_argument, 333 },
{ "split-prefix", ko_required_argument, 334 },
{ "no-end-flt", ko_no_argument, 335 },
{ "bed", ko_required_argument, 336 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -101,7 +102,7 @@ int main(int argc, char *argv[])
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, n_parts;
char *fnw = 0, *rg = 0, *s;
char *fnw = 0, *fn_bed = 0, *rg = 0, *s;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
mm_idx_t *mi;
@@ -188,6 +189,7 @@ int main(int argc, char *argv[])
else if (c == 333) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
else if (c == 334) opt.split_prefix = o.arg; // --split-prefix
else if (c == 335) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
else if (c == 336) fn_bed = o.arg; // --bed-prefer
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary
@@ -342,6 +344,7 @@ int main(int argc, char *argv[])
fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
if (fn_bed) mm_idx_read_bed(mi, fn_bed);
if (mm_verbose >= 3) mm_idx_stat(mi);
if (!(opt.flag & MM_F_FRAG_MODE)) {
for (i = o.ind + 1; i < argc; ++i)