From 68b5c6dfbd0df436663a9f042f60bc9a0d7d8254 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 | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/svreader/pindel.py b/svreader/pindel.py
index fa5ccb8..fbc79a5 100644
--- a/svreader/pindel.py
+++ b/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):
--
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