def argument_parse(self, config_file=None):
"""
config_file: including all tools path
this function set attribute to self, all tools in config file will be set
#tools
bwa = /home/zhluo/miniconda3/bin/bwa
samtools = /home/zxchen/anaconda3/bin/samtools
picard = /home/zhluo/Software/picard.jar
bbmap = /home/zhluo/miniconda3/bin/filterbyname.sh
het_raw=/home/zyang/software/heteroplasmy.pyflow/heteroplasmy.mle.py
het_filter=/home/zyang/software/heteroplasmy.pyflow/heteroplasmy.mle.filter.py
bamleftalign= /home/zhluo/miniconda3/bin/bamleftalign
#human reference hg19
ref_genome = /home/zyang/mit/ref/chrM.fa
whole_genome = /home/zhluo/Project/mitch/autism/ref/GRCh37.p13.genome.fa
"""
arguments = Basic.read_arguments(arg_file=config_file)
for key in arguments:
setattr(self, key, arguments[key])
