From a609a07f8cff4662b39f25fb042f7fff730807b9 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 7 Jul 2018 10:26:08 -0500
Subject: [PATCH] optionally output unmapped query in PAF

---
 format.c  | 4 ++++
 main.c    | 2 ++
 map.c     | 9 +++++++++
 minimap.h | 1 +
 4 files changed, 16 insertions(+)

diff --git a/format.c b/format.c
index f38289f..a4b8234 100644
--- a/format.c
+++ b/format.c
@@ -259,6 +259,10 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
 void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag)
 {
 	s->l = 0;
+	if (r == 0) {
+		mm_sprintf_lite(s, "%s\t%d", t->name, t->l_seq);
+		return;
+	}
 	mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
 	if (mi->seq[r->rid].name) mm_sprintf_lite(s, "%s", mi->seq[r->rid].name);
 	else mm_sprintf_lite(s, "%d", r->rid);
diff --git a/main.c b/main.c
index 1b25541..22d55e3 100644
--- a/main.c
+++ b/main.c
@@ -60,6 +60,7 @@ static struct option long_options[] = {
 	{ "lj-min-ratio",   required_argument, 0, 0 },   // 30
 	{ "score-N",        required_argument, 0, 0 },   // 31
 	{ "eqx",            no_argument,       0, 0 },   // 32
+	{ "paf-no-hit",     no_argument,       0, 0 },   // 33
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -179,6 +180,7 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==30) opt.min_join_flank_ratio = atof(optarg); // --lj-min-ratio
 		else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
 		else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
+		else if (c == 0 && long_idx ==33) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
 		else if (c == 0 && long_idx == 14) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
 		} else if (c == 0 && long_idx == 15) { // --secondary
diff --git a/map.c b/map.c
index 08dfe60..0864c09 100644
--- a/map.c
+++ b/map.c
@@ -496,6 +496,15 @@ static void *worker_pipeline(void *shared, int step, void *in)
 						mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
 					mm_err_puts(p->str.s);
 				}
+				if (s->n_reg[i] == 0) {
+					if (p->opt->flag & MM_F_OUT_SAM) {
+						mm_write_sam2(&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);
+						mm_err_puts(p->str.s);
+					} else if (p->opt->flag & MM_F_PAF_NO_HIT) {
+						mm_write_paf(&p->str, mi, t, 0, 0, p->opt->flag);
+						mm_err_puts(p->str.s);
+					}
+				}
 				if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) { // write an unmapped record
 					mm_write_sam2(&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);
 					mm_err_puts(p->str.s);
diff --git a/minimap.h b/minimap.h
index 3590173..c1a9267 100644
--- a/minimap.h
+++ b/minimap.h
@@ -32,6 +32,7 @@
 #define MM_F_OUT_MD        0x1000000
 #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_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2