new pindel specific filter

svreader/pindel.py

@@ -320,7 +320,7 @@ class PindelRecord(SVRecord):
             calls.append(calldata)
         return calls
 
-    def MaxIndSupportingRP(self):
+    def MaxIndividualSupport(self):
         max_ind_supp = 0
         for s in self.__samples:
             ad = s["up_var_read_supp"] + s["down_var_read_supp"]
@@ -331,7 +331,7 @@ class PindelRecord(SVRecord):
         alt = [vcf.model._SV(self.sv_type)]
         info = {"SVLEN": self.sv_len, "SVTYPE": self.sv_type}
 
-        info["MAX_IND_SU"] = self.MaxIndSupportingRP()
+        info["MAX_IND_SU"] = self.MaxIndividualSupport()
         info["VSAMPLES"] = ",".join(self.variantSamples())
 
         info.update(self.Modinfo)
@@ -388,15 +388,14 @@ class PindelReader(SVReader):
     #     # Sudmant et al 2015 SuppInfo
     #     return (record.length() > 60)
     def SpecificFilterPass(self, record):
-        if (abs(record.start-record.end+1) >= 2000 or
-            record.MaxIndSupportingRP() <= 4):
+         # new pindel specific filter
+        if record.length() >= 800 or record.length() <= 60:
+            return False
+        elif record.MaxIndividualSupport() <= 3:
             return False
         else:
             return True
 
-
-###### Old Stuff ############################
-
     def remove_duplicate(self, records):
         """
            returns a vector of records where duplicates were removed
@@ -430,7 +429,6 @@ class PindelReader(SVReader):
             return True
         return False
 
-###### Old Stuff ############################
 
 class PindelWriter(SVWriter):
     def __init__(self, file_name, reference_contigs, template_reader):