juliangehring

# Download ICGC public release in a semi-automated manner
#
# Usage: ./download_icgc.sh
#
# Be sure to check the original link to contain all summary files
#   https://dcc.icgc.org/releases/release_23/Summary
# and list all files you want from the cohorts in contents().
#
# There may be different contents in the project folders. Check a couple, e.g.:
#   https://dcc.icgc.org/releases/release_23/Projects/CLLE-ES

juliangehring

## let's create a sequence, and look at the 10th element which is 0.1
s1 = (1:100)/100
s1[10] ## -> 0.1
s1[10] == 0.1 ## -> TRUE, makes sense

s2 = seq(0.01, 1, by = 0.01) ## should be the same as 's1'
all.equal(s1, s2) ## -> TRUE, still looks good
identical(s1, s2) ## -> FALSE, a bit worrisome 

s2[10] ## -> 0.1

juliangehring

scanVcfParamInteractive <- function(file) {

    asdf <- function(x) {
        df = data.frame(Field = rownames(x), Description = x$Description, Type = x$Type)
    }

    charIfNull <- function(x) {
        if(is.null(x)) {
            return(character())
        }