old_contents: # -*- coding: utf-8 -*-
  #
  #  This file is part of Sequana software
  #
  #  Copyright (c) 2016 - Sequana Development Team
  #
  #  File author(s):
  #      Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
  #      Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>, 
  #          <d.desvillechabrol@gmail.com>
  #
  #  Distributed under the terms of the 3-clause BSD license.
  #  The full license is in the LICENSE file, distributed with this software.
  #
  #  website: https://github.com/sequana/sequana
  #  documentation: http://sequana.readthedocs.io
  #
  ##############################################################################
  
  import os
  import shutil
  
  import pandas as pd
  
  from reports import HTMLTable
  from sequana.report_main import BaseReport
  
  
  class VariantReport(BaseReport):
      """
      """
      def __init__(self, csv_file, output_filename, directory="report", **kargs):
          super(VariantReport, self).__init__(jinja_filename="variant/index.html",
                  directory=directory, output_filename=output_filename, 
                  **kargs)
          self.jinja['title'] = "Variants Report"
          self.csv = csv_file
  
      def set_data(self, data):
          self.vcf_record = data
  
      def parse(self):
          df = self.vcf_record.vcf_to_csv(self.csv)
          self.jinja["csv_link"] = self.csv.split("/")[-1]
  
          self.jinja["nb_variant"] = len(df)
  
          shutil.copy(self.vcf_record.filename, self.directory)
          self.jinja["vcf_link"] = self.vcf_record.filename.split("/")[-1] 
  
          html = HTMLTable(df)
          self.jinja['vcf_filter'] = html.to_html(index=False)
  
new_contents: # -*- coding: utf-8 -*-
  #
  #  This file is part of Sequana software
  #
  #  Copyright (c) 2016 - Sequana Development Team
  #
  #  File author(s):
  #      Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
  #      Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>, 
  #          <d.desvillechabrol@gmail.com>
  #
  #  Distributed under the terms of the 3-clause BSD license.
  #  The full license is in the LICENSE file, distributed with this software.
  #
  #  website: https://github.com/sequana/sequana
  #  documentation: http://sequana.readthedocs.io
  #
  ##############################################################################
  
  import os
  import shutil
  
  import pandas as pd
  
  from reports import HTMLTable
  from sequana.report_main import BaseReport
  
  
  class VariantReport(BaseReport):
      """
      """
      def __init__(self, csv_file, output_filename, directory="report", **kargs):
          super(VariantReport, self).__init__(jinja_filename="variant/index.html",
                  directory=directory, output_filename=output_filename, 
                  **kargs)
          self.jinja['title'] = "Variants Report"
          self.csv = csv_file
  
      def set_data(self, data):
          self.vcf_record = data
  
      def parse(self):
          df = self.vcf_record.df
          self.jinja["csv_link"] = self.csv.split("/")[-1]
  
          self.jinja["nb_variant"] = len(df)
  
          shutil.copy(self.vcf_record.filename, self.directory)
          self.jinja["vcf_link"] = self.vcf_record.filename.split("/")[-1] 
  
          html = HTMLTable(df)
          self.jinja['vcf_filter'] = html.to_html(index=False)
  
subject: Add filter_vcf update