The python files have inconsistent use of spaces and tabs that fails when I run it on my system (sherlock computing cluster at Stanford with python/3.6.1). I have fixed this with the command "autopep8 -i *.py" to conform to PEP8 standards.
In addition, we often use sequence files with the ending ".fq.gz" which is not recognized by fastqgz_to_counts.py. I have added this filetype.
The python files have inconsistent use of spaces and tabs that fails when I run it on my system (sherlock computing cluster at Stanford with python/3.6.1). I have fixed this with the command "autopep8 -i *.py" to conform to PEP8 standards.
In addition, we often use sequence files with the ending ".fq.gz" which is not recognized by fastqgz_to_counts.py. I have added this filetype.