From e5ba99b6fdb29a547f072c78cc2f794892e2115c Mon Sep 17 00:00:00 2001
From: kristinebilgrav <77359122+kristinebilgrav@users.noreply.github.com>
Date: Mon, 6 Feb 2023 16:35:06 +0100
Subject: [PATCH 1/3] Update tiddit_contig_analysis.pyx

bug fix
---
 tiddit/tiddit_contig_analysis.pyx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tiddit/tiddit_contig_analysis.pyx b/tiddit/tiddit_contig_analysis.pyx
index 35c2904..ae31441 100644
--- a/tiddit/tiddit_contig_analysis.pyx
+++ b/tiddit/tiddit_contig_analysis.pyx
@@ -39,13 +39,13 @@ def read_contigs(aligned_contigs,prefix,sample_id,min_size):
 		elif read.has_tag("XA") and not (read.is_supplementary or read.is_secondary):
 			XA=read.get_tag("XA")
 			if XA.count(";") == 1:
-				if "-" in XA:
-					XA=XA.replace("-","")
+				if ",-" in XA:
+					XA=XA.replace(",-",",")
 					xa_list=XA.split(",")
 					xa_list.insert(2,"-")
 					XA=",".join(xa_list)
 				else:
-					XA=XA.replace("+","")
+					XA=XA.replace(",+",",")
 					xa_list=XA.split(",")
 					xa_list.insert(2,"+")
 					XA=",".join(xa_list)

From bee73bda121a34636a0d8d3b51f2d6ace930e0d0 Mon Sep 17 00:00:00 2001
From: kristinebilgrav <77359122+kristinebilgrav@users.noreply.github.com>
Date: Mon, 6 Feb 2023 16:35:42 +0100
Subject: [PATCH 2/3] Update setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 2421302..e1ba6f1 100644
--- a/setup.py
+++ b/setup.py
@@ -20,7 +20,7 @@
 
 setup(
     name = 'tiddit',
-    version = '3.5.1',
+    version = '3.5.2',
 
     url = "https://github.com/SciLifeLab/TIDDIT",
     author = "Jesper Eisfeldt",

From 502ee52b4633775e8c94d315add9ecc9dc780662 Mon Sep 17 00:00:00 2001
From: kristinebilgrav <77359122+kristinebilgrav@users.noreply.github.com>
Date: Mon, 6 Feb 2023 16:36:29 +0100
Subject: [PATCH 3/3] Update __main__.py

---
 tiddit/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tiddit/__main__.py b/tiddit/__main__.py
index 95ed918..697f652 100644
--- a/tiddit/__main__.py
+++ b/tiddit/__main__.py
@@ -17,7 +17,7 @@
 import tiddit.tiddit_contig_analysis as tiddit_contig_analysis
 
 def main():
-	version="3.5.1"
+	version="3.5.2"
 	parser = argparse.ArgumentParser("""tiddit-{}""".format(version),add_help=False)
 	parser.add_argument("--sv"	 , help="call structural variation", required=False, action="store_true")
 	parser.add_argument("--cov"        , help="generate a coverage bed file", required=False, action="store_true")