From e18935fbad76f72674741c86ab27f5b0e8017470 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 29 Mar 2025 22:43:44 -0400
Subject: [PATCH] r1230: make juncevla work for paired-end SAM

---
 misc/paftools.js | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/misc/paftools.js b/misc/paftools.js
index bfc9960..79b3682 100755
--- a/misc/paftools.js
+++ b/misc/paftools.js
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.28-r1209';
+var paftools_version = '2.28-r1230-dirty';
 
 /*****************************
  ***** Library functions *****
@@ -2494,6 +2494,10 @@ function paf_junceval(args)
 		} else { // SAM
 			ctg_name = t[2], pos = parseInt(t[3]) - 1, cigar = t[5];
 			var flag = parseInt(t[1]);
+			if (flag & 1) {
+				if (flag & 0x40) qname += '/1';
+				else if (flag & 0x80) qname += '/2';
+			}
 			if (flag&0x100) continue; // secondary
 		}