old_contents: #!/usr/bin/python
  import os
  import inspect
  
  
  """
  This code can be modified to suit your specific environment
    Such as reference file locations
    Software locations
    
  PLEASE DO NOT SEND ME PULL REQUESTS INCLUDING ANY MODIFICATIONS YOU MAKE TO THIS FILE, I WILL ALMOST CERTAINLY 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 + '/reference/mm10_index/mm10.index',
  							}
  		
  		#THIS MUST BE VERSION 0.1.19 OR THE PIPELINE MAY NOT WORK#
  		self.samtools = '/home/k4zhang/softwares/samtools-0.1.19/samtools'
  		
  		self.bowtieOptions =	[
  								'bowtie',
  								 '-p 8',
  								 '-S', 
  								 '-t',
  								 '-n 2',
  								 '-e 70',
  								 '-m 1',
  								 '--phred33-quals',
  								 '--best',
  								 '--strata',
  								 '--chunkmbs 200',
  								]
  
  
  
  
  		
  		
  		
  		
  		
  		
  class Count:
  	
  	def __init__(self):
  		self.currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
  		
  		self.binDict =	{
  						'hg38': self.currentdir + '/reference/hg38.varbin.gc.content.25k.bowtie.k36.txt',
  						'mm10': self.currentdir + '/reference/mm10.varbin.gc.content.25k.bowtie.k36.txt',
  						}
  		
  		self.chromDict =	{
  							'hg38': self.currentdir + '/reference/hg38.chrom.sizes.txt',
  							'mm10': self.currentdir + '/reference/mm10.chrom.sizes.txt',
  							}
  
  
  
  
  
  
new_contents: #!/usr/bin/python
  import os
  import inspect
  import sys
  
  
  """
  This code can be modified to suit your specific environment
    Such as reference file locations
    Software locations
    
  PLEASE DO NOT SEND ME PULL REQUESTS INCLUDING ANY MODIFICATIONS YOU MAKE TO THIS FILE, I WILL ALMOST CERTAINLY 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 + '/reference/mm10_index/mm10.index',
  							}
  		
  		#THIS MUST BE VERSION 0.1.19 OR THE PIPELINE MAY NOT WORK#
  		self.samtools = '/home/k4zhang/softwares/samtools-0.1.19/samtools'
  		
  		self.bowtieOptions =	[
  								'bowtie',
  								 '-p 8',
  								 '-S', 
  								 '-t',
  								 '-n 2',
  								 '-e 70',
  								 '-m 1',
  								 '--phred33-quals',
  								 '--best',
  								 '--strata',
  								 '--chunkmbs 200',
  								]
  
  
  
  
  		
  		
  		
  		
  		
  		
  class Count:
  	
  	def __init__(self):
  		self.currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
  		
  		self.binDict =	{
  						'hg38': self.currentdir + '/reference/hg38.varbin.gc.content.25k.bowtie.k36.txt',
  						'mm10': self.currentdir + '/reference/mm10.varbin.gc.content.25k.bowtie.k36.txt',
  						}
  		
  		self.chromDict =	{
  							'hg38': self.currentdir + '/reference/hg38.chrom.sizes.txt',
  							'mm10': self.currentdir + '/reference/mm10.chrom.sizes.txt',
  							}
  
  
  
  
  
  
  		
  		
  		
  class Segment:
  	
  	def __init__(self):
  		self.currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
  		
  		self.binDict =	{
  						'hg38': self.currentdir + '/reference/hg38.varbin.fullRef.25k.bowtie.k36.txt',
  						'mm10': self.currentdir + '/reference/mm10.varbin.fullRef.25k.bowtie.k36.txt',
  						}
  		
  	#	self.chromDict =	{
  	#						'hg38': self.currentdir + '/reference/hg38.chrom.sizes.txt',
  	#						'mm10': self.currentdir + '/reference/mm10.chrom.sizes.txt',
  	#						}
  	
  		self.statsmodelsLocation = '/home/srohrbac/research/packages/statsmodels-0.6.1'
  		sys.path.append(self.statsmodelsLocation)
  		
  		
  		
  		
  		
  		
  
subject: Update config.py