new_contents: import collections
  
  def readFileMap(fileName):
    result = collections.OrderedDict()
    
    with open(fileName, 'r') as f:
      for line in f:
        parts = line.rstrip().split('\t')
        if len(parts) > 1:
          result[parts[1]] = parts[0]
  
    return(result)
  
subject: read file map from file list generated by pipeline