Use the valid input file to get the header information.

def main(args):
  of = sys.stdout
  if args.output and args.output[-4:] == '.bam':
    cmd = 'samtools view -Sb - -o '+args.output
    pof = Popen(cmd.split(),stdin=PIPE)
    of = pof.stdin
  elif args.output:
    of = open(args.output,'w')
  """Use the valid input file to get the header information."""

  header = None
  if args.HQ:
    cmd = 'samtools view -H '+args.HQ
    sys.stderr.write(cmd+"\n")
    header = Popen(cmd.split(),stdout=PIPE).communicate()[0]
    of.write(header)
  if (not header) and args.HQCorrected:
    cmd = 'samtools view -H '+args.HQCorrected
    sys.stderr.write(cmd+"\n")
    header = Popen(cmd.split(),stdout=PIPE).communicate()[0]
    of.write(header)
  if (not header) and args.AQ:
    cmd = 'samtools view -H '+args.AQ
    sys.stderr.write(cmd+"\n")
    header = Popen(cmd.split(),stdout=PIPE).communicate()[0]
    of.write(header)
  if (not header) and args.AQCorrected:
    cmd = 'samtools view -H '+args.AQCorrected
    sys.stderr.write(cmd+"\n")
    header = Popen(cmd.split(),stdout=PIPE).communicate()[0]
    of.write(header)
  if (not header) and args.subreads:
    cmd = 'samtools view -H '+args.subreads
    sys.stderr.write(cmd+"\n")
    header = Popen(cmd.split(),stdout=PIPE).communicate()[0]
    of.write(header)
  if (not header) and args.subreadsCorrected:
    cmd = 'samtools view -H '+args.subreadsCorrected
    sys.stderr.write(cmd+"\n")
    header = Popen(cmd.split(),stdout=PIPE).communicate()[0]
    of.write(header)

  _nameprog = re.compile('^(\S+)')
  negative_filter = set() # remove these
  """ Next read throught he alignments THAT ALIGNED in order of priority"""
  negative_filter = get_best_set(negative_filter,'-F 4',of,args,True)
  """After traversing all the aligned reads we can do it all over again
     this time with the unaligned portion of reads"""

  """ Finally go through the reads that did NOT ALIGN to get anything left"""
  get_best_set(negative_filter,'-f 4',of,args,False)
  if args.output and args.output[-4:] == '.bam':
    pof.communicate()
  else:
    of.close()