From 0f8a164bd39824a3cd25a8521e54b3d7b60abada Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 25 Oct 2014 23:08:29 -0400
Subject: [PATCH] bugfix: .ctw not generated properly

---
 bwa-postalt.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bwa-postalt.js b/bwa-postalt.js
index 1e8bd06..b538552 100644
--- a/bwa-postalt.js
+++ b/bwa-postalt.js
@@ -482,7 +482,7 @@ function bwa_postalt(args)
 			}
 			if (ovlp_alt.length > 0) { // add other unreported hits
 				for (var i = 0; i < ovlp_alt.length; ++i)
-					if (ovlp_alt[i][0] <= rpt_start && rpt_end <= ovlp_alt[i][1])
+					if (ovlp_alt[i][0] <= rpt_start && rpt_end <= ovlp_alt[i][1] && alts[ovlp_alt[i][2]] == null)
 						alts[ovlp_alt[i][2]] = [0, 0];
 			}