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r938: added --sam-hit-only; resolved #377

This commit is contained in:
Heng Li 2019-04-30 22:40:36 -04:00
parent 97f67a2a0a
commit c2aec88b84
4 changed files with 8 additions and 2 deletions
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2
main.c
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@ -65,6 +65,7 @@ static ko_longopt_t long_options[] = {
{ "max-chain-iter", ko_required_argument, 339 }, { "max-chain-iter", ko_required_argument, 339 },
{ "junc-bed", ko_required_argument, 340 }, { "junc-bed", ko_required_argument, 340 },
{ "junc-bonus", ko_required_argument, 341 }, { "junc-bonus", ko_required_argument, 341 },
{ "sam-hit-only", ko_no_argument, 342 },
{ "help", ko_no_argument, 'h' }, { "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' }, { "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' }, { "version", ko_no_argument, 'V' },
@ -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 == 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 == 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) 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 else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1); yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary } else if (c == 315) { // --secondary

2
map.c
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@ -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_write_paf3(&p->str, mi, t, r, km, p->opt->flag, s->rep_len[i]);
mm_err_puts(p->str.s); 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_PAF_NO_HIT) || ((p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_SAM_HIT_ONLY))) { // output an empty hit, if requested
if (p->opt->flag & MM_F_OUT_SAM) 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]); 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 else

1
minimap.h
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@ -35,6 +35,7 @@
#define MM_F_PAF_NO_HIT 0x8000000 // output unmapped reads to PAF #define MM_F_PAF_NO_HIT 0x8000000 // output unmapped reads to PAF
#define MM_F_NO_END_FLT 0x10000000 #define MM_F_NO_END_FLT 0x10000000
#define MM_F_HARD_MLEVEL 0x20000000 #define MM_F_HARD_MLEVEL 0x20000000
#define MM_F_SAM_HIT_ONLY 0x40000000
#define MM_I_HPC 0x1 #define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2 #define MM_I_NO_SEQ 0x2

5
minimap2.1
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@ -1,4 +1,4 @@
.TH minimap2 1 "28 Feburary 2019" "minimap2-2.16-dirty (r934)" "Bioinformatics tools" .TH minimap2 1 "30 April 2019" "minimap2-2.16-dirty (r938)" "Bioinformatics tools"
.SH NAME .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences
@ -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 set to `*'. Warning: some paftools.js commands may not work with such output
for the moment. for the moment.
.TP .TP
.B --sam-hit-only
In SAM, don't output unmapped reads.
.TP
.B --version .B --version
Print version number to stdout Print version number to stdout
.SS Preset options .SS Preset options