From 52def33c47e5c5cfb170a76ccde2296cc15fd2ea Mon Sep 17 00:00:00 2001
From: alexpan00 <alexpan0098@gamil.com>
Date: Thu, 13 Jun 2024 15:49:45 +0200
Subject: [PATCH] Fixed a bug in the assignation of CAGE peaks of trasncripts
 in the negative strand

---
 sqanti3_qc.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/sqanti3_qc.py b/sqanti3_qc.py
index 9960645..0b5c235 100755
--- a/sqanti3_qc.py
+++ b/sqanti3_qc.py
@@ -2204,7 +2204,10 @@ def find(self, chrom, strand, query, search_window=10000):
             if strand=='-' and start0<int(query) and end1<int(query):
                 continue
 ##
-            within_out = (start0<=query<end1)
+            if strand == "+":
+                within_out = (start0<=query<end1)
+            if strand == "-":
+                within_out = (start0<query<=end1)
             if within_out:
                 w = 'TRUE'
             else: