From 95807a22246d9541ebc9023417089f3cfae7aeb8 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 13 Oct 2024 23:58:33 -0400
Subject: [PATCH] added "junc_pen" to python accordingly

---
 python/cmappy.pxd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/cmappy.pxd b/python/cmappy.pxd
index 47855fe..05bb7a9 100644
--- a/python/cmappy.pxd
+++ b/python/cmappy.pxd
@@ -39,7 +39,7 @@ cdef extern from "minimap.h":
 		int transition
 		int sc_ambi
 		int noncan
-		int junc_bonus
+		int junc_bonus, junc_pen
 		int zdrop, zdrop_inv
 		int end_bonus
 		int min_dp_max