From 98c23bc6d20ea6e8ca3de22f2525046fde6feeab Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 19 Mar 2024 09:55:16 -0400
Subject: [PATCH] r1194: output NM in sam2paf

---
 misc/paftools.js | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/misc/paftools.js b/misc/paftools.js
index 67819e9..481436f 100755
--- a/misc/paftools.js
+++ b/misc/paftools.js
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.27-r1193';
+var paftools_version = '2.27-r1194-dirty';
 
 /*****************************
  ***** Library functions *****
@@ -1887,7 +1887,10 @@ function paf_sam2paf(args)
 		// optional tags
 		var type = flag&0x100? 'S' : 'P';
 		var tags = ["tp:A:" + type];
-		if (NM != null) tags.push("mm:i:"+mm);
+		if (NM != null) {
+			tags.push("NM:i:"+NM);
+			tags.push("mm:i:"+mm);
+		}
 		tags.push("gn:i:"+(I[1]+D[1]), "go:i:"+(I[0]+D[0]), "cg:Z:" + t[5].replace(/\d+[SH]/g, ''));
 		if (cs_str != null) tags.push("cs:Z:" + cs_str);
 		else if (cs.length > 0) tags.push("cs:Z:" + cs.join(""));