adding gidget config file to git ignore list.
adding initial configuration file handling
picking up latest changes from 'develop' and merging into feature/gidget-config.
updating branch with lastest changes from 'develop' into feature/gidget-config
adding interpolation to config file; adding some programmatically-generated defaults for config; test of using config to set env vars in subprocess.
adding documentation on ConfigParser's case conversion.
cleaning up and archiving currently unused scripts for the MAF pipeline,
per discussion with @liype
updated to new rppa annotation file
changed example string
changed example string
Merging branch 'release/0.0.12' into develop (version bump)
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
modified so that calling scripts can specify whether a "public" or a "private"
feature matrix is being built
fixed example string
added illuminaga_rnaseqv2 platform, updated RPPA antibody filename
added code to make features relative to the days_to_sample_procurement
minor change in how blank tokens are handled
fixed a bug that was happening when numJobs==1
modified to be able to just run current or refactor by itself
modifications to always use the UUID column.  exception are the agilent platforms where some of the archives predate use of the UUID