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

lh3 · May 1, 2019 · c2aec88 · c2aec88
1 parent 97f67a2
commit c2aec88
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Showing 4 changed files with 8 additions and 2 deletions.
diff --git a/main.c b/main.c
@@ -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' },
@@ -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

diff --git a/map.c b/map.c
@@ -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_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)
 						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

diff --git a/minimap.h b/minimap.h
@@ -35,6 +35,7 @@
 #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  0x40000000
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2

diff --git a/minimap2.1 b/minimap2.1
@@ -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
 .PP
 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
 for the moment.
 .TP
+.B --sam-hit-only
+In SAM, don't output unmapped reads.
+.TP
 .B --version
 Print version number to stdout
 .SS Preset options