From 315795eefd5fb1d968a5bd77ddac470b36282e5b Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 10 Sep 2022 08:48:57 -0400
Subject: [PATCH] skip unmapped lines

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

diff --git a/misc/paftools.js b/misc/paftools.js
index 636f8ad..95bf7ea 100755
--- a/misc/paftools.js
+++ b/misc/paftools.js
@@ -3195,6 +3195,7 @@ function paf_paf2gff(args) {
 	var hid = 1, last_name = null;
 	while (file.readline(buf) >= 0) {
 		var m, t = buf.toString().split("\t");
+		if (t[5] == '*') continue; // skip unmapped lines
 
 		if (t[0] != last_name) last_name = t[0], hid = 1;
 		else ++hid;