text: #!/usr/local/bin/python
  import sys
  import subprocess
  import os
  import numpy as np
  
  if len(sys.argv) < 3:
      print 'usage:' + sys.argv[0] + ' <max> <out file> <in bam 1> <in bam 2> <..>'
      exit(1)
  
  max_c = int(sys.argv[1])
  out_file = sys.argv[2]
  
  o = open('.exclude.tmp','w')
  
  for i in range(3,len(sys.argv)):
      bam_file = sys.argv[i]
      coverage_file = bam_file + '.coverage'
  
      f = open(coverage_file, 'r')
      for l in f:
          a = l.rstrip().split('\t')
          if (int(a[3]) > max_c):
              o.write(l)
      f.close()
  o.close()
              
  p = subprocess.Popen(\
          'cat .exclude.tmp | ' \
          'sort -S 20G -k1,1 -k2,2n | ' \
          'bedtools merge -i stdin -d 50 ' \
          '> ' + out_file, shell=True)
  os.waitpid(p.pid, 0)
  os.unlink('.exclude.tmp')
  