diff --git a/svreader/pindel.py b/svreader/pindel.py index 2b51cf1ea586ec1cc524e9dbf0c1ef20af0dae33..f6a5e92a8502bc93d5ce6e66adad186a2a759709 100644 --- a/svreader/pindel.py +++ b/svreader/pindel.py @@ -308,7 +308,7 @@ 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"] @@ -319,7 +319,7 @@ 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) @@ -377,12 +377,14 @@ class PindelReader(SVReader): # return (record.length() > 60) def SpecificFilterPass(self, record): # fILTER - if (abs(record.start-record.end+1) >= 2000 and - record.MaxIndSupportingRP() <= 3): + if sv.length() >= 800 or sv.length() <= 60: + return False + elif record.MaxIndividualSupport() <= 3: return False else: return True + def remove_duplicate(self, records): """ returns a vector of records where duplicates were removed