old_contents: # import python packages
  import time
  
  # import classes
  import VCF_Analyzer
  import FDR 
  
  # set up the vcf and chisq filepaths
  # TODO enter the correct paths
  vcf_path = "N:/app dev/scoville research/program files/dev migration for windows/vcf files/Ali_w_767.vcf";
  chisq_path = "C:/Users/David/Documents/GitHub/mg-gap/mg-gap/mg-gap/support files/chisq.txt";
  
  # run the vcf parser for SNP window of 1
  
  # TODO there's some code here for timing, then a lot of code that is
  # commented out, code that includes the Window class. 
  # Ask - Is this important? 
  
  # feed the median value back through b processing, then b* 
  # need to hold on to the data for FDR though
  median = 6
  if median > 0:
      # TODO need to find equivalent "Convert" method in python see commented code below
      snpList = VCF_Analyzer.SNP_list(Convert.ToInt32(median), vcf_path, chisq_path)
      print("Re-analyzing for B* based on median window size ", median, " @ ", time.ctime)
  
      # Start the FDR process
      # This should be a user config variable in the future if they would prefer any different settings
      # TODO maybe create user input for fdr_input value
      fdr_input = 0.05
      print("Running FDR analysis at ", fdr_input, "...")
      # TODO save this fdrlist to a "tab" separated values, use a .csv, file with headers 
      fdrlist = FDR.Process(snpList, fdr_input)
      
      # Start getting the annotations !! May stop here for the purposes of 
      # this program. TODO ask about this. Yes we canstop here.
  
  
  
  
  # TODO Look up "Convert" method equivalent in python
  """
  namespace System
  {
      //
      // Summary:
      //     Converts a base data type to another base data type.
      public static class Convert {
  
          public static int ToInt32(int value);
          //
          // Summary:
          //     Converts the value of the specified 64-bit signed integer to an equivalent 32-bit
          //     signed integer.
          //
          // Parameters:
          //   value:
          //     The 64-bit signed integer to convert.
          //
          // Returns:
          //     A 32-bit signed integer that is equivalent to value.
          //
          // Exceptions:
          //   T:System.OverflowException:
          //     value is greater than System.Int32.MaxValue or less than System.Int32.MinValue.
  }
  """
  
new_contents: # import python packages
  import time
  
  # import classes
  import VCF_Analyzer
  import FDR 
  
  # set up the vcf and chisq filepaths
  # TODO enter the correct paths
  vcf_path = "N:/app dev/scoville research/program files/dev migration for windows/vcf files/Ali_w_767.vcf";
  chisq_path = "C:/Users/David/Documents/GitHub/mg-gap/mg-gap/mg-gap/support files/chisq.txt";
  
  # run the vcf parser for SNP window of 1
  
  # TODO there's some code here for timing, then a lot of code that is
  # commented out, code that includes the Window class. 
  # Ask - Is this important? 
  
  # feed the median value back through b processing, then b* 
  # need to hold on to the data for FDR though
  median = 6
  if median > 0:
      # TODO need to find equivalent "Convert" method in python see commented code below
      snpList = VCF_Analyzer.SNP_list(Convert.ToInt32(median), vcf_path, chisq_path)
      print("Re-analyzing for B* based on median window size ", median, " @ ", time.ctime)
  
      # Start the FDR process
      # This should be a user config variable in the future if they would prefer any different settings
      # TODO maybe create user input for fdr_input value
      fdr_input = 0.05
      print("Running FDR analysis at ", fdr_input, "...")
      # TODO save this fdrlist to a "tab" separated values, use a .csv, file with headers 
      fdrlist = FDR.Process(snpList, fdr_input)
      
      # Start getting the annotations !! May stop here for the purposes of 
      # this program. TODO ask about this. Yes we canstop here.
  
      # TODO Something that may be of interest later. Connect to pythosome site to get Gene, description, and RNA SEQ data.
  
  
  # TODO Look up "Convert" method equivalent in python
  """
  namespace System
  {
      //
      // Summary:
      //     Converts a base data type to another base data type.
      public static class Convert {
  
          public static int ToInt32(int value);
          //
          // Summary:
          //     Converts the value of the specified 64-bit signed integer to an equivalent 32-bit
          //     signed integer.
          //
          // Parameters:
          //   value:
          //     The 64-bit signed integer to convert.
          //
          // Returns:
          //     A 32-bit signed integer that is equivalent to value.
          //
          // Exceptions:
          //   T:System.OverflowException:
          //     value is greater than System.Int32.MaxValue or less than System.Int32.MinValue.
  }
  """
  
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