Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add option --sam-hit-only #377

Closed
wants to merge 2 commits into from
Closed

add option --sam-hit-only #377

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7bff7eb
add option --sam-hit-only
vejnar Apr 12, 2019
95b8a58
Resolve merge conflict incrementing option number to 342
vejnar Apr 30, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions main.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@ static ko_longopt_t long_options[] = {
{ "max-chain-iter", ko_required_argument, 339 },
{ "junc-bed", ko_required_argument, 340 },
{ "junc-bonus", ko_required_argument, 341 },
{ "sam-hit-only", ko_no_argument, 342 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
Expand Down Expand Up @@ -207,6 +208,7 @@ int main(int argc, char *argv[])
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 == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary
Expand Down
2 changes: 1 addition & 1 deletion map.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -589,7 +589,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_write_paf3(&p->str, mi, t, r, km, p->opt->flag, s->rep_len[i]);
mm_err_puts(p->str.s);
}
} else if (p->opt->flag & (MM_F_OUT_SAM|MM_F_PAF_NO_HIT)) { // output an empty hit, if requested
} else if (p->opt->flag & ((MM_F_OUT_SAM&!MM_F_SAM_HIT_ONLY)|MM_F_PAF_NO_HIT)) { // output an empty hit, if requested
if (p->opt->flag & MM_F_OUT_SAM)
mm_write_sam3(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag, s->rep_len[i]);
else
Expand Down
5 changes: 3 additions & 2 deletions minimap.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,9 @@
#define MM_F_COPY_COMMENT 0x2000000
#define MM_F_EQX 0x4000000 // use =/X instead of M
#define MM_F_PAF_NO_HIT 0x8000000 // output unmapped reads to PAF
#define MM_F_NO_END_FLT 0x10000000
#define MM_F_HARD_MLEVEL 0x20000000
#define MM_F_SAM_HIT_ONLY 0x10000000 // output only mapped reads to SAM
#define MM_F_NO_END_FLT 0x20000000
#define MM_F_HARD_MLEVEL 0x40000000

#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2
Expand Down
3 changes: 3 additions & 0 deletions minimap2.1
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -489,6 +489,9 @@ In PAF, output unmapped queries; the strand and the reference name fields are
set to `*'. Warning: some paftools.js commands may not work with such output
for the moment.
.TP
.B --sam-hit-only
In SAM, only output mapped queries.
.TP
.B --version
Print version number to stdout
.SS Preset options
Expand Down