Nothing
# These are temporary methods, that are likely to be replaced by
# methods from the Rsamtools package in near future.
# takes a character vector with CIGAR strings, returns a list
extendedCIGARToList <- function(cigars) {
indList = gregexpr("[A-Z]", cigars)
cigarList = list()
for (l in 1:length(indList)) {
ind = c(0, indList[[l]])
s = cigars[[l]]
m = integer()
for (i in 2:length(ind)) {
m[i-1] = as.integer(substr(s, ind[i-1]+1, ind[i]-1))
names(m)[i-1] = substr(s, ind[i], ind[i])
}
cigarList[[l]] = m
}
names(cigarList) = names(cigars)
return(cigarList)
}
# takes a list with converted CIGAR string (see above) and returns a character vector
listToExtendedCIGAR <- function(cigarList){
cigars = vector(mode="character")
for (l in 1:length(cigarList))
cigars[l] = paste(paste(cigarList[[l]], names(cigarList[[l]]), sep=""), collapse="")
names(cigars) = names(cigarList)
return(cigars)
}
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