From 107a9870eff9b27f266fe0544301f1ccfea2a547 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 23 Nov 2011 23:18:51 -0500
Subject: [PATCH] incorrect mate pos in BWA-SW SE mode

---
 bwtsw2_aux.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c
index 4ac11fd..6a283e2 100644
--- a/bwtsw2_aux.c
+++ b/bwtsw2_aux.c
@@ -496,7 +496,8 @@ static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks
 			for (k = 0; k < q->n_cigar; ++k)
 				ksprintf(&str, "%d%c", q->cigar[k]>>4, (opt->hard_clip? "MIDNHHP" : "MIDNSHP")[q->cigar[k]&0xf]);
 		} else ksprintf(&str, "\t0\t*");
-		ksprintf(&str, "\t%s\t%d\t%d\t", q->mchr==q->chr? "=" : (q->mchr<0? "*" : bns->anns[q->mchr].name), q->mpos+1, q->isize);
+		if (!is_pe) kputs("\t*\t0\t0\t", &str);
+		else ksprintf(&str, "\t%s\t%d\t%d\t", q->mchr==q->chr? "=" : (q->mchr<0? "*" : bns->anns[q->mchr].name), q->mpos+1, q->isize);
 		// get the sequence begin and end
 		beg = 0; end = ks->l;
 		if (opt->hard_clip) {