modified so that the name of the "aux" directory can be specified at the
command line -- eg "aux-manuscript" or "aux-test" -- if unspecified it will
default to the current assumed name which is simply "aux"
new sample META file for loading into RE database
added some stuff at the end of this script to make a preliminary META
data file that is almost, but not quite ready to use for importing into RE
Updating mutation summary generation to parse MAF protein change codes for in-frame deletions.  AA pos output column takes the first position mentioned in the deletion; "to aa" and "from aa" are left blank in this case.
detailed notes for manual MAF and binarization pipelines
updated list of tumors based on DCC public data directories
adding error check (yes, should be done for most subcommands eventually)
adding more informative error message.
modified loose matching to allow partial substring matching anywhere
rather than only prefix-matching
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
Create CHANGELOG.md
(cleaning up extraneous text)
formatting
formatting
Update CHANGELOG.md
Update CHANGELOG.md
bumping version number before release.
added bcgsc.ca as a possible source for MAF files
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
Clarifying script name with extension.