modified: setup.py

	modified:   svdb/__main__.py
	modified:   svdb/readVCF.py

Author: J35P312

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="[email protected]",

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",

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