From 0e55d097137fc0b8c5ad4f166d133ac0a3903bb2 Mon Sep 17 00:00:00 2001
From: Juan Esteban Arango Ossa <juanes.ao@gmail.com>
Date: Thu, 23 May 2024 16:19:58 -0400
Subject: [PATCH] fix file handler issue when running as cli (#4)

---
 mergesvvcf/mergedfile.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/mergesvvcf/mergedfile.py b/mergesvvcf/mergedfile.py
index 30ee1d6..42e36aa 100644
--- a/mergesvvcf/mergedfile.py
+++ b/mergesvvcf/mergedfile.py
@@ -270,8 +270,9 @@ def passed_variant(record):
         "String",
         "Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)",
     )
-
-    outfile = open(outfile,'w')
+    # outfile should be a file handler. if it's a file name open it
+    if isinstance(outfile, str):
+        outfile = open(outfile,'w')
     print(outvcf.header, end="", file=outfile)
 
     for variant in sorted(calldict, key=operator.itemgetter(0)):