old_contents: #!/usr/bin/python
  
  
  
  """
  This code can be modified to suit your specific environment
    Such as file locations
    Execultable locations
    
  PLEASE DO NOT SEND ME PULL REQUESTS INCLUDING ANY MODIFICATIONS YOU MAKE TO THIS FILE, I WILL REJECT THEM
    If I have missed adding in a specific reference, let me know by message
  """
  
  
  
  
new_contents: #!/usr/bin/python
  import os
  import inspect
  
  
  """
  This code can be modified to suit your specific environment
    Such as file locations
    Execultable locations
    
  PLEASE DO NOT SEND ME PULL REQUESTS INCLUDING ANY MODIFICATIONS YOU MAKE TO THIS FILE, I WILL REJECT THEM
    If I have missed adding in a specific reference, let me know by message
  """
  
  
  class Map:
  	
  	def __init__(self):
  		self.currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
  		
  		self.indexDict =	{
  							'hg38': self.currentdir + '/reference/hg38_index/hg38.index',
  							'mm10': self.currentdir + '/referencemm10_index/mm10.index',
  							}
  		
  		self.samtools = '/home/k4zhang/softwares/samtools-0.1.19/samtools'
  		
  ###		self.bowtie = 
  
  
  
  
subject: Update config.py