From 99f5ca9e5eed648e91d4059de673d85b70dd703e Mon Sep 17 00:00:00 2001
From: KareemMarzouk <bkmarzouk@outlook.com>
Date: Fri, 26 Jan 2024 16:11:00 +0000
Subject: [PATCH] use vanilla sort

---
 src/SOPRANO/core/analysis.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/SOPRANO/core/analysis.py b/src/SOPRANO/core/analysis.py
index 5519d89..56bc9eb 100755
--- a/src/SOPRANO/core/analysis.py
+++ b/src/SOPRANO/core/analysis.py
@@ -82,7 +82,8 @@ def _sum_possible_across_region(
 
     pipe(  # TODO: This appears to be a memory bottleneck ...
         ["awk", '{print "test_"$2"_"$3"\t0\t1\t"$0}', trans_regs.as_posix()],
-        ["sortBed", "-i", "stdin"],
+        # ["sortBed", "-i", "stdin"],
+        ["sort"],  # , "-k", "1,1", "-k2,2n"],
         ["mergeBed", "-i", "stdin", "-c", "7,8", "-o", "sum,sum"],
         ["cut", "-f1,4,5"],
         output_path=sum_trans_regs,