Merge pull request #17 from hrovira/develop

Small fixes to develop branch
added a debug warning and a couple of lines so that the script
returns to the current working directory when it finishes
modified so that a separate methylation data file (eg from Synapse)
can be used rather than obtained/parse from the dcc-snapshot (which
is the default mode of operation)
modified so that the output file name will include part of the feature
name rather than just the class label, when the class label is not
very distinctive (eg YES/NO or 1/0 etc)
note: NOT working version.  Turning on perl 'strict' and finding MANY critical scope issues.  Code changed to syntactically correct but will require futher analysis to get into correctly working state.
adding debugging help
changing function to use and return values from hash references
massive rewrite to correctly pass global variables between subroutines.  UNTESTED.  syntax ok
using dated data directory rather than renamed database files, for now.
Correcting env var usage.
correcting env var usage
updating to more generic input file name:
restoring tsv python utility
restoring previously archived file; needed by updateMAF.sh
updating maf processing script for current pipeline
more code cleanup attempts
most quietest warnings yet! :)
updating executable flag for bash script
Adding automation upon download for stripping header from uniprot secondar->primary accession number mapping file