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Commit 2f124943 authored by Thomas Faraut's avatar Thomas Faraut
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fixing bug in lumpy parser

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svreader/__init__.py
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− 1
View file @ 2f124943
...@@ -213,7 +213,7 @@ class SVReader(object): ...@@ -213,7 +213,7 @@ class SVReader(object):
if (sv[4] != "." if (sv[4] != "."
and sv[4] != "-1" and sv[4] != "-1"
and float(sv[-1]) < cutoff_proximity): and float(sv[-1]) < cutoff_proximity):
print("-".join(sv)) #print("-".join(sv))
excluded[sv[3]] = 1 excluded[sv[3]] = 1
vcf_records_filtered = [] vcf_records_filtered = []
......
svreader/lumpy.py
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− 1
View file @ 2f124943
...@@ -184,7 +184,7 @@ class LumpyReader(SVReader): ...@@ -184,7 +184,7 @@ class LumpyReader(SVReader):
# Filtering criteria more than 4 PE # Filtering criteria more than 4 PE
# see # see
# http://bcb.io/2014/08/12/validated-whole-genome-structural-variation-detection-using-multiple-callers # http://bcb.io/2014/08/12/validated-whole-genome-structural-variation-detection-using-multiple-callers
return record.MaxIndSupportingRP() > 4 and record.sr >0 return record.MaxIndSupportingRP() > 4 and record.sr[0] >0
class LumpyWriter(SVWriter): class LumpyWriter(SVWriter):
......
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