improving the first cut at the META loading file
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
added another line for the "interesting_scores" information
fixed typo (in a comment)
updated, with modifications to handle most MAF files as well as the
*.ncm and/or *.ncm.with_uniprot files that are part of the MAF pipeline
changed output file name construction
modified so that the scoreCatFeat-v2 tasks are run in the background,
also this is now run on the pre-split FMx as well as the tumor-only
subsets
added abi and solid platform types
removed obsolete code related to processing multiple tumors at once
fixed bug that was left over from when these types of scripts were intended
to handle multiple tumors at once, also took back out the change that tried
to run the survival analysis on the non-split (tumor-only) feature matrices
(that really cannot work for a feature matrix with patients having multiple
samples)
fixed two error statements to more accurately indicate what the error is
bumping version for release
bug fix in findCode()
fairly extensive fixing up ... when the "chop-feat" stuff was added to eliminate
"unimportant" parts of a feature name, it didn't initially handle all of the data
types correctly -- especially CLIN/SAMP features... now hopefully everything is working
commented out the two calls to the scripts that get protected data
added a few lines to create a "summary" file for the FMx
added ucs to list of cancer types
added the public/private argument to the command-line for this script
fixed usage info
changed how/when fmp10B* and fmp15B* scripts are called