Major Description
Right now pipeline.pl is well over 2000 lines long and extremely difficult to navigate.
I propose the following
- All ENV is refactored into an pipeline_environment file
- All Command line parsing and definitions are refactored into a pipeline_cli file
- Sanity checking is refactored into a pipeline_sanity_check file
- Dependenct Variable Checking is refactored into pipeline_dependent_variable_setting file
- filter and preprocess corpora is refactored into pipeline_filter_preprocess_corpora
- pipeline_subsampling becomes a file
- pipeline_alignment becomes a file
- pipeline_parsing becomes a file
- pipeline_thrax becomes a file
- pipeline_tuning becomes a file
- pipeline_testing becomes a file
- pipeline_subreoutines becomes a file