text: #!/usr/bin/env python
  import argparse
  parser = argparse.ArgumentParser(description="")
  parser.add_argument("bam", help='regex of files to use, must be put in quotes, e.g. "test.*.sam" ' )
  args = parser.parse_args()
  
  import glob
  import os
  import sys
  import re
  from collections import Counter
  import pysam 
  
  
  
  def readSam(myfile):
  	bam = pysam.AlignmentFile(myfile)
  	nameLength = {}
  	for idx,read in enumerate(bam.fetch(until_eof=True)):
  		nameLength[read.query_name] = read.infer_query_length()
  	return(nameLength)
  
  names = []
  reads = {}
  for bam in glob.glob(args.bam):
  	sys.stderr.write(bam + "\n")
  	dic =  readSam(bam)
  	reads.update(dic)
  	names+=dic.keys()
  
  counts = Counter(names)
  
  
  bad = 0.0
  badN = 0.0
  good = 0.0
  goodN = 0.0
  for readid in counts:
  	num = counts[readid]
  	if(num > 1):
  		badN += 1
  		bad += reads[readid]
  	else:
  		goodN += 1
  		good += reads[readid]
  
  #print(goodN, good/goodN)
  #print(badN, bad/badN)
  
  
  print(badN/(goodN+badN))
  
  