storage = new SAMFileWriterStorage((SAMFileWriterStub)stub,file);
else
storage = new SAMFileWriterStorage((SAMFileWriterStub)stub);
}
else if(stub instanceof VariantContextWriterStub) {
VariantContextWriterStub vcfWriterStub = (VariantContextWriterStub)stub;
if( file != null )
storage = new VariantContextWriterStorage(vcfWriterStub,file);
else
storage = new VariantContextWriterStorage(vcfWriterStub);
}