From b69663b4b16bf731c519a11e6bb4bf4b2349ed6a Mon Sep 17 00:00:00 2001
From: Yueyao Gao <gaoyueya@broadinstitute.org>
Date: Tue, 2 Jul 2024 23:01:29 -0400
Subject: [PATCH] bug fix for padded section

---
 CNV-Profiler/CNV-Profiler.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CNV-Profiler/CNV-Profiler.wdl b/CNV-Profiler/CNV-Profiler.wdl
index 26f8272..e3798bd 100644
--- a/CNV-Profiler/CNV-Profiler.wdl
+++ b/CNV-Profiler/CNV-Profiler.wdl
@@ -131,7 +131,7 @@ task GetPaddedCnvBed {
 
         with open('padded_cnv.bed', 'a') as f:
             for interval in padded_cnv_interval_list:
-                chrom = interval.split(':')[0]
+                chr = interval.split(':')[0]
                 start = interval.split(':')[1].split('-')[0]
                 end = interval.split(':')[1].split('-')[1]
                 f.write(f"{chr}\t{start}\t{end}" + '\n')