code: def editheaders():
      
      # Read stdin - this will be the output from samtools view
      for line in fileinput.input():
          try:
              # Get the flag value from the input
              columns = line.split('\t')
              # The FLAG is in the second column
              flag = int(columns[1])
              # Subtracts 256 from the flag if the & bitwise operator evaluates to true
              # See http://www.tutorialspoint.com/python/bitwise_operators_example.htm
              # For the test case, flags of 256 became 0, and flags of 272 became 16
              columns[1] = str((flag - 256) if (flag & 256) else flag)
              # update = [columns[0], str(flag), columns[2:]]
              sys.stdout.write('\t'.join(columns))
          # Don't fail on IOErrors, or ValueErrors, and still print line to stdout
          except (IOError, ValueError):
              sys.stdout.write(line)
              pass
      # Try except statements to get rid of file closing errors
      try:
          sys.stdout.flush()
          sys.stdout.close()
      except:
          pass
      try:
          sys.stderr.close()
      except:
          pass
docs: Edits the headers of SAM files to remove 'secondary alignments