From 0cc3cdca27f050fb80a19c90d25ecc6ab0b0907b Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 7 Apr 2024 17:12:31 -0400
Subject: [PATCH] ignore filtered SVs in sveval

---
 misc/paftools.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/misc/paftools.js b/misc/paftools.js
index 24405e38..3bd95ff5 100755
--- a/misc/paftools.js
+++ b/misc/paftools.js
@@ -3240,6 +3240,7 @@ function paf_sveval(args)
 			if (bed != null && bed[t[0]] == null) continue;
 			if (t[4] == '<INV>' || t[4] == '<INVDUP>') continue; // no inversion
 			if (/[\[\]]/.test(t[4])) continue; // no break points
+			if (t[6] != "." && t[6] != "PASS") continue;
 			var st = parseInt(t[1]) - 1, en = st + t[3].length;
 			// parse svlen
 			var b = _paf_get_alen(t), svlen = b[0];