From 196b50dde3a345720a55ae6d751a395525adef73 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 23 Nov 2011 23:39:59 -0500
Subject: [PATCH] optionally mark multi-part hits as secondary

---
 bwtsw2_aux.c | 2 +-
 main.c       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c
index 863d23d..400fcf2 100644
--- a/bwtsw2_aux.c
+++ b/bwtsw2_aux.c
@@ -489,7 +489,7 @@ static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks
 		bsw2aux_t *q = b->aux + i;
 		int j, beg, end, type = 0;
 		// print mandatory fields before SEQ
-		ksprintf(&str, "%s\t%d", ks->name, q->flag);
+		ksprintf(&str, "%s\t%d", ks->name, q->flag | (opt->multi_2nd && i? 0x100 : 0));
 		ksprintf(&str, "\t%s\t%ld", q->chr>=0? bns->anns[q->chr].name : "*", (long)q->pos + 1);
 		if (p->l == 0) { // not a repetitive hit
 			ksprintf(&str, "\t%d\t", q->pqual);
diff --git a/main.c b/main.c
index 10e3314..69379ed 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.0-r91-dev"
+#define PACKAGE_VERSION "0.6.0-r97-dev"
 #endif
 
 static int usage()