stevemussmann/admixturePipeline: Admixture Pipeline v2.0

Pre-release for new admixturePipeline version.

v2.0 combines admixturePipeline with my admixture_cv_sum and distruct-rerun repositories.

New features include:

• python3 compatibility
• added distructRerun.py and cvSum.py
• distructRerun.py can now execute distruct on drawparams files
• New options and flexibility are included for selecting a color palette in distructRerun.py
• distructRerun.py now performs functions that previously required additional bash commands to be run by the user

Bug fixes:

• The correct input population list for CLUMPAK is now generated when using the blacklist option or excluding individuals due to high amounts of missing data in admixturePipeline.
• Fixed a condition in which admixturePipeline would erroneously include .Q files from subdirectories.
• Fixed parsing of boolean command line options
• Various minor bug fixes

Experimental options:

• distructRerun.py now has an option that may allow you to re-run distruct on STRUCTURE data that was analyzed in CLUMPAK. Option is not robustly tested.