⭐ indicates changes to the algorithm that could potentially change results, though best efforts were made for 1:1 conversion
🔲 indicates changes i hope to reverse and are only 'temp fixes'
- Originally ran 2to3 in commit a5d062fab68f8bbbebc2bbe9f4192b47b451146e
- removed explicit versioning in the Makefile since py3 version still in dev
- 🔲 removed version checks in setup.py and obsolete setuptools
- changed default references from s3://cgl-pipeline-inputs to s3://protect-data
- this s3 bucket is pay to access, however currently s3am is untested and only automatically converted
- ⭐⭐ common.py chromosome sorting
- docker image decodes to utf-8
- IOBase check rather than file
- some binary vs string adaptations
- ⭐ change obselete ix to loc
- 🔲 quick fix: running into problem with '80.0' default for cores. can't figure out where the default is coming from so manual changes:
- string.maketrans is obselete, str.maketrans is better
- changed gunzip file write to use a library (faster?)