From c8c538089fd5f05d891db3686d83a79c97d5adbf Mon Sep 17 00:00:00 2001
From: J35P312 <jesper.eisfeldt@scilifelab.se>
Date: Fri, 21 Apr 2023 13:13:03 +0200
Subject: [PATCH] 	modified:   setup.py 	modified:   svdb/__main__.py 
 modified:   svdb/readVCF.py

---
 setup.py         | 2 +-
 svdb/__main__.py | 2 +-
 svdb/readVCF.py  | 7 +++++++
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 41fbfb5..d3f8aec 100644
--- a/setup.py
+++ b/setup.py
@@ -19,7 +19,7 @@
     ext_modules = []
 
 setup(name='svdb',
-      version='2.8.1',
+      version='2.8.2',
       url="https://github.com/J35P312/SVDB",
       author="Jesper Eisfeldt",
       author_email="jesper.eisfeldt@scilifelab.se",
diff --git a/svdb/__main__.py b/svdb/__main__.py
index 6bbc5cc..d3d98f0 100644
--- a/svdb/__main__.py
+++ b/svdb/__main__.py
@@ -46,7 +46,7 @@ def make_query_calls (args, queries, keyword):
         query_module.main(args)
 
 def main():
-    version = "2.8.1"
+    version = "2.8.2"
     parser = argparse.ArgumentParser(
         """SVDB-{}, use the build module to construct databases, use the query module to query the database usign vcf files, or use the hist module to generate histograms""".format(version), add_help=False)
     parser.add_argument('--build', help="create a db",
diff --git a/svdb/readVCF.py b/svdb/readVCF.py
index 1834001..c85d450 100644
--- a/svdb/readVCF.py
+++ b/svdb/readVCF.py
@@ -107,6 +107,13 @@ def readVCFLine(line):
             chrA = chrB
             chrB = chrT
             posA, posB = posB, posA
+
+        #intrachromosomal variant
+        if chrA == chrB:
+            if posB < posA:
+                posA, posB = posB, posA
+
+
         event_type = "BND"
 
     return chrA, posA, chrB, posB, event_type, description, format