new_contents: #!/usr/bin/env python
  
  import os
  import sys
  import argparse
  
  if __name__ == "__main__":
      parser = argparse.ArgumentParser()
      parser.add_argument('-s', '--samples_file', help="Input list of sample/library names to search for")
      args = parser.parse_args()
  
      samples = list()
      with open(args.samples_file, 'r') as samples_file:
          samples = samples_file.read().splitlines()
      root_dir = os.getcwd()
  
      # Check FinalBams
      os.chdir("./FinalBAMs")
      sys.stdout.write("Missing final aligned BAM files:\n")
      for sample in samples:
          if os.path.isfile("{}.recalibrated.sorted.bam".format(sample)):
              sys.stdout.write("{}\n".format(sample))
      os.chdir(root_dir)
  
      # # Check MuTect
      # os.chdir("./MuTect")
      # sys.stdout.write("Missing MuTect VCFs:\n")
      # for sample in samples:
      #     if not os.path.isfile("{}.mutect.vcf".format(sample)):
      #         sys.stdout.write("{}\n".format(sample))
      # os.chdir(root_dir)
      #
      # # Check VarDict
      # os.chdir("./VarDict")
      # sys.stdout.write("Missing VarDict VCFs:\n")
      # for sample in samples:
      #     if not os.path.isfile("{}.vardict.vcf".format(sample)):
      #         sys.stdout.write("{}\n".format(sample))
      # os.chdir(root_dir)
      #
      # # Check Scalpel
      # os.chdir("./Scalpel")
      # sys.stdout.write("Missing Scalpel VCFs:\n")
      # for sample in samples:
      #     if not os.path.isdir("{}-scalpel-output".format(sample)):
      #         sys.stdout.write("No Folder: {}\n".format(sample))
      #     else:
      #         os.chdir("{}-scalpel-output/".format(sample))
      #         if not os.path.isfile("variants.indel.vcf"):
      #             sys.stdout.write("No Variants file: {}\n".format(sample))
      #         os.chdir("..")
      # os.chdir(root_dir)
      #
      # # Check FreeBayes
      # os.chdir("./FreeBayes")
      # sys.stdout.write("Missing FreeBayes VCFs:\n")
      # for sample in samples:
      #     if not os.path.isfile("{}.freebayes.vcf".format(sample)):
      #         sys.stdout.write("{}\n".format(sample))
      # os.chdir(root_dir)
  
      # Check GEMINI Databases
      # os.chdir("./GEMINI")
      # sys.stdout.write("Missing GEMINI databases:\n")
      # for sample in samples:
      #     if not os.path.isfile("{}.snpEff.GRCh37.75.db".format(sample)):
      #         sys.stdout.write("{}\n".format(sample))
      # os.chdir(root_dir)
  
subject: Add script for finding duplicate results