modified where expression_matrix_mimat output goes.  also added platform name to addition feature
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
merge refactored code into gidget.  also adds modifications to miRNA processing to put intermediary output into the final output directory
update genelist location for methylation and rppa
cleaned up code, set row and col to not sort and modified test of current vs. refactor to print out run time difference
Updating branch feature/miRNAEMMimatChange with current changes from the more recent 'develop' branch.
Merging branch 'feature/miRNAEMMimatChange' into develop.

Places output from miRNA script into current working directory, rather the TCGA repository directory.
fixed infinite loop trap -- nFpJ was sometimes 0 if the overall job wasn't very big ...
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
minor clean-up
Merge remote-tracking branch 'origin/feature/refactor' into feature/refactor to be upto date with sheila's updates
merged with sheila's updates to develop
synch the refactor branch with the current changes in the develop branch
unmerge new_Level3_matrix.py, use the current develop branch version
modified so it won't try to annotate a platform feature
modified script pipeline scripts to run the refactored code
removed merge conflicts and also fixed a problem with tsvIO.uniqueFeatureLabels() that was always adding a number to every feature
added specific error if can't get topDir
fixes to match parse_all_xml.py, fix bad indentation and fix postprocess() to consistently use the member varirable
update comment for processDirectories() to add overrides