#NEWLINE# def __init__( self , variantAnnotationSetId , baseDir ) : #NEWLINE# #INDENT# self . _dataset = datasets . AbstractDataset ( 'ds' ) #NEWLINE# self . _datarepo = datarepo . FileSystemDataRepository ( 'tests/data' ) #NEWLINE# super ( VariantAnnotationSetTest , self ) . __init__ ( variantAnnotationSetId , baseDir ) #NEWLINE# self . _variantSet = variants . HtslibVariantSet ( self . _dataset , 'vs' , self . _dataPath , None ) #NEWLINE# self . _variantRecords = [ ] #NEWLINE# self . _referenceNames = set ( ) #NEWLINE# for vcfFile in glob . glob ( os . path . join ( self . _dataPath , '*.vcf.gz' ) ) : #NEWLINE# #INDENT# if self . _isAnnotated ( ) : #NEWLINE# #INDENT# self . _readVcf ( variantAnnotationSetId ) #NEWLINE# #UNINDENT# #UNINDENT# self . _isCsq = self . _hasConsequenceField ( )