From e5616c87eb21146e3e56001957b447a123d224ff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontus.hojer@scilifelab.se>
Date: Wed, 22 Jan 2025 17:48:43 +0100
Subject: [PATCH] generate target_bed in output_dir if given

---
 cnvlib/batch.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/cnvlib/batch.py b/cnvlib/batch.py
index 845675aa..46e1b7b4 100644
--- a/cnvlib/batch.py
+++ b/cnvlib/batch.py
@@ -75,6 +75,9 @@ def batch_make_reference(
                 access_arr = access.do_access(fasta)
                 # Take filename base from FASTA, lacking any other clue
                 target_bed = os.path.splitext(os.path.basename(fasta))[0] + ".bed"
+                if output_dir:
+                    target_bed = os.path.join(output_dir, target_bed)
+
                 tabio.write(access_arr, target_bed, "bed3")
             else:
                 raise ValueError(