From d4b5dfc2974cd0a6c087eb53242ae7e3cefe8a19 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 23 Oct 2017 14:09:32 -0400
Subject: [PATCH] r533: added --no-pairing

to prevent the use of any pairing information for paired-end reads.
---
 main.c    | 4 +++-
 map.c     | 7 ++++++-
 minimap.h | 1 +
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/main.c b/main.c
index 0d02673..4d5618c 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.3-r531"
+#define MM_VERSION "2.3-r533-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -41,6 +41,7 @@ static struct option long_options[] = {
 	{ "secondary",      optional_argument, 0, 0 },
 	{ "cs",             optional_argument, 0, 0 },
 	{ "end-bonus",      required_argument, 0, 0 },
+	{ "no-pairing",     no_argument,       0, 0 },
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -135,6 +136,7 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
 		else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
 		else if (c == 0 && long_idx ==17) opt.end_bonus = atoi(optarg); // --end-bonus
+		else if (c == 0 && long_idx ==18) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
 		else if (c == 0 && long_idx == 14) { // --frag
 			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
 				opt.flag |= MM_F_FRAG_MODE;
diff --git a/map.c b/map.c
index 35efa6d..a31bceb 100644
--- a/map.c
+++ b/map.c
@@ -414,7 +414,12 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
 		qseqs[j] = s->seq[off + j].seq;
 		quals[j] = is_sr? s->seq[off + j].qual : 0;
 	}
-	mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, quals, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
+	if (s->p->opt->flag & MM_F_INDEPEND_SEG) {
+		for (j = 0; j < s->n_seg[i]; ++j)
+			mm_map_frag(s->p->mi, 1, &qlens[j], &qseqs[j], &quals[j], &s->n_reg[off+j], &s->reg[off+j], b, s->p->opt, s->seq[off+j].name);
+	} else {
+		mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, quals, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
+	}
 	for (j = 0; j < s->n_seg[i]; ++j) // flip the query strand and coordinate to the original read strand
 		if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1)))) {
 			int k, t;
diff --git a/minimap.h b/minimap.h
index e1dbf88..058c1e3 100644
--- a/minimap.h
+++ b/minimap.h
@@ -22,6 +22,7 @@
 #define MM_F_NO_PRINT_2ND  0x4000
 #define MM_F_2_IO_THREADS  0x8000
 #define MM_F_LONG_CIGAR    0x10000
+#define MM_F_INDEPEND_SEG  0x20000
 
 #define MM_IDX_MAGIC   "MMI\2"