where to find ichorCNA.R and pysam version

[ryao-mdanderson]

Dear author @gavinha

I have two questions:

1. Section : Scripts and Executables, where to find ichorCNA.R?
   ichorCNA.R (ichorCNA tool for normalizing and correcting read coverage)

2. TitanCNA/scripts/snakemake/code/countPysam.py does not work with pysam version 0.21.0
   I installed the application as a conda enviroment, I am not able to install pysam version 0.11.2.1 , Is any workaround?

$ python scripts/snakemake/code/countPysam.py --help
Traceback (most recent call last):
File "$HOME/TitanCNA/scripts/snakemake/code/countPysam.py", line 7, in
norm_hetpsns = sys.argv[2]
IndexError: list index out of range

Thanks,
Rong Yao