From adaa808283605d79e562e314d61e2988961228a1 Mon Sep 17 00:00:00 2001
From: Yueyao Gao <gaoyueya@broadinstitute.org>
Date: Tue, 2 Jul 2024 22:24:28 -0400
Subject: [PATCH] bed file format bug fix

---
 CNV-Profiler/CNV-Profiler.wdl | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CNV-Profiler/CNV-Profiler.wdl b/CNV-Profiler/CNV-Profiler.wdl
index 79dad90..808bbdf 100644
--- a/CNV-Profiler/CNV-Profiler.wdl
+++ b/CNV-Profiler/CNV-Profiler.wdl
@@ -131,7 +131,10 @@ task GetPaddedCnvBed {
 
         with open('padded_cnv.bed', 'a') as f:
             for interval in padded_cnv_interval_list:
-                f.write(interval + '\n')
+                chrom = interval.split(':')[0]
+                start = interval.split(':')[1].split('-')[0]
+                end = interval.split(':')[1].split('-')[1]
+                f.write("{chr}\t{start}\t{end}" + '\n')
         CODE
     >>>
     runtime {