.gitignore

+**__pycache__

svreader/delly.py

@@ -202,7 +202,7 @@ class DellyReader(SVReader):
         # see http://bcb.io/2014/08/12/validated-whole-genome-structural-variation-detection-using-multiple-callers
         # TODO : should we modifiy this in order to account for individual
         #       specific filtering (e.g pe > 5 at least for an individual)
-        return (record.pe > 5 or (record.pe > 0 and record.sr > 0))
+        return (record.pe > 5 or record.sr > 0))
 
     def bnd_merge(sef, svtype, records):
         """

svreader/lumpy.py

@@ -98,6 +98,10 @@ class LumpyRecord(SVRecord):
     def record(self):
         return self.__record
 
+    @property
+    def sr(self):
+        return self.__record.info['SR']
+
     def getAltBND(self):
         ''' extract second breakend chr,pos from ALT field '''
         alt = self.__record.ALT[0]
@@ -180,7 +184,7 @@ class LumpyReader(SVReader):
         # Filtering criteria more than 4 PE
         # see
         # http://bcb.io/2014/08/12/validated-whole-genome-structural-variation-detection-using-multiple-callers
-        return (record.MaxIndSupportingRP() > 4)
+        return record.MaxIndSupportingRP() > 4 and record.sr >0
 
 
 class LumpyWriter(SVWriter):