From d34684ca63cee908eeac095f90ce58dbb9232181 Mon Sep 17 00:00:00 2001
From: Thomas Faraut <Thomas.Faraut@inra.fr>
Date: Thu, 27 Feb 2020 13:54:05 +0100
Subject: [PATCH] new implementation of get samples in lumpy
---
svreader/annotation.py | 1 +
svreader/lumpy.py | 12 +++++++++---
2 files changed, 10 insertions(+), 3 deletions(-)
diff --git a/svreader/annotation.py b/svreader/annotation.py
index c1aa1cf..1197d14 100644
--- a/svreader/annotation.py
+++ b/svreader/annotation.py
@@ -145,6 +145,7 @@ class AnnotateRecord(VCFRecord):
def add_supporting_infos(self):
supp_reads = self.variant_read_support()
num_supp_samples = self.num_variant_samples()
+ #print(supp_reads, num_supp_samples)
try:
self.record.info['MAX_SUPP_READS'] = supp_reads
self.record.info['NUM_SUPP_SAMPLES'] = num_supp_samples
diff --git a/svreader/lumpy.py b/svreader/lumpy.py
index 618f6a4..20d2d6e 100644
--- a/svreader/lumpy.py
+++ b/svreader/lumpy.py
@@ -181,10 +181,15 @@ class LumpyReader(SVReader):
def AreSamplesSpecified(self):
return 1
+ # def getOrderedSamples(self):
+ # if not hasattr(self.vcf_reader, "samples"):
+ # return []
+ # return self.vcf_reader.samples
+
def getOrderedSamples(self):
- if not hasattr(self.vcf_reader, "samples"):
- return []
- return self.vcf_reader.samples
+ samples = self.vcf_reader.header.samples
+ sample_names = [sample.rsplit('.')[0] for sample in samples]
+ return sample_names
def SpecificFilterPass(self, record):
# First try after sensibility analysis with Mathieu
@@ -219,4 +224,5 @@ class LumpyWriter(SVWriter):
if self._isopen:
self.vcf_writer.close()
else: # nothing was written
+ # Make sure appropriate samples are added to the vcf
self._dumpemptyvcf()
--
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