Merge branch 'newfilter' of forgemia.inra.fr:svdetection/svlib into newfilter

svreader/Annotate.py

@@ -130,8 +130,8 @@ class AnnotatedRecordSample(object):
 class VCFReader(SVReader):
 
     def __init__(self, file_name, sv_to_report=None):
+<<<<<<< HEAD
         super(VCFReader, self).__init__(file_name)
-        self.vcf_reader = VariantFile(file_name)
         self.filename = file_name
         self.sv_to_report = sv_to_report
         self.vcf_reader = VariantFile(file_name)
@@ -172,7 +172,6 @@ class VCFReader(SVReader):
         self.addFilter("LOWSUPPORT",
                        "total supp reads < 5 or supp samples < 2")
 
-
     def getOrderedSamples(self):
         samples = self.vcf_reader.header.samples
         sample_names = [sample.rsplit('.')[0] for sample in samples]

svreader/pindel.py

@@ -396,6 +396,7 @@ class PindelReader(SVReader):
         else:
             return True
 
+
     def remove_duplicate(self, records):
         """
            returns a vector of records where duplicates were removed