Features/ft 885 refactor acgh survival analysis

Refactor the analysis pipeline for the aCGH survival analysis.
are you sure there are never any duplicates in phenotypedataIds and colnames(calls)? In case of duplicates pmatch may not behave as expected:
pmatch(c("a","a","b"),c("a","a","f","x"),duplicates.ok=T)
[1]  1  1 NA
> pmatch(c("a","a","b"),c("a","a","f","x"),duplicates.ok=F)
[1]  1  2 NA
> pmatch(c("a","a","b"),c("a","f","x"),duplicates.ok=F)
[1]  1 NA NA
> pmatch(c("a","a","b"),c("a","f","x"),duplicates.ok=T)
[1]  1  1 NA
default for duplicates.ok = FALSE