hotfix: fix infinite loop in FMx construction
(from develop 32f02fd21bd706b70e70e404b70cb34771a9403a)
commented out some debug print statements
added code to use Gencode database for annotation, also made changes
to try and make sure everything is case-insensitive
added patient barcode to a couple of debug/log-file print statements
commented out some debug print statements
cleaned up script a little bit, changed the handling of multiple gene
expression platforms somewhat (eg COAD and READ have GA and  HiSeq data
from UNC, UCEC also has a mix of platforms and annotation pipeline
versions, LAML has data from both UNC and BCGSC, etc)
changed the way multiple RNAseq platforms are handled
added new platform: unc_edu_illuminaga_rnaseqv2
updated comments to reflect new platform (unc_edu_illuminaga_rnaseqv2)
added new platform (unc_edu_illuminaga_rnaseqv2)
updated instructions
standard config file to be used when there is methylation data from
the 27k platform (also includes config information for all other platforms)
config file to be used when only 450k methylation data is available
this script prepares the 450k data for downstream inclusion in the
feature matrix ... this should generally be used only for tumor types
that have ONLY 450k data ... note also that this takes 8-14 hours to
run and so should only be run when there is new 450k data
new script for computing correlations between METH features and GEXP
or MIRN features in order to decide which METH/GEXP/MIRN features to
keep (rather than only doing high-variability filtering)
removed the 450k meth stuff from this script, not the right place for it
modified versions of these scripts for the 450k-only tumors
Adding version info as documentation comment.
Renaming script without version in script name; will be tracked in version control and documened in comments.
Adding mutation summary file, by @bradybernard.