create_geneAdj:I have added a function to compute SampleColours that needs more work and
a seqTech variable to designate the sequencing tech used.
The file input procedure has also been modified.

create_metadata_structure: not much has changed except for adding colon and rectum
metadata. I made sure the variable names (colnames) in the colon rectum data tables
match before rbinding them together.

identify_hypermutated: I added some extramodifications to indelSNVratio and others to enable plotting by cancerType,
but they could be used for plotting according to other metadata now.
I still need to clean up the silentVsnonSilentRatio variable names as these actaully refer to Indel:SNVs.

Signed-off-by: SutherlandRuss <SutherlandRuss@googlemail.com>