From a65df1e7e93b630a2b72c983bd2abb9267358aa2 Mon Sep 17 00:00:00 2001
From: Thomas Faraut <Thomas.Faraut@inra.fr>
Date: Thu, 31 Oct 2019 14:16:32 +0100
Subject: [PATCH] new pindel specific filter
---
svreader/pindel.py | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/svreader/pindel.py b/svreader/pindel.py
index 2b51cf1..f6a5e92 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
--
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