Commit da1c431a authored by Sudeep Sahadevan's avatar Sudeep Sahadevan

bump data.table version to 1.11.8 for native .gz support

parent 63255097
......@@ -10,7 +10,7 @@ Maintainer: Hentze bioinformatics team <biohentze@embl.de>
Description: Differential expression analysis of windows for next-generation sequencing data like eCLIP or iCLIP data.
Imports:
BiocGenerics,
data.table,
data.table(>= 1.11.8),
GenomeInfoDb,
GenomicRanges,
methods,
......
......@@ -37,15 +37,7 @@
if(checkWindowNumber){
neededCols <- c(neededCols,'window_number')
}
gzlen <- grep(pattern = '\\.gz',ignore.case = TRUE,x=fname)
platform <- Sys.info()[['sysname']]
if(gzlen>0 && platform=='Windows'){
annTable <- read.table(gzfile(fname),sep="\t",stringsAsFactors=FALSE,header=TRUE)
}else if(gzlen>0){ # assuming that zcat binary is installed in Linux and Mac distributions
annTable <- fread(input=paste('zcat',fname),sep="\t",stringsAsFactors = FALSE,header=TRUE)
}else if (gzlen==0){
annTable <- fread(fname,sep="\t",stringsAsFactors = FALSE,header=TRUE)
}
annTable <- fread(fname,sep="\t",stringsAsFactors = FALSE,header=TRUE)
missingCols <- setdiff(neededCols,colnames(annTable))
if(length(missingCols)>0 & checkWindowNumber){
stop('Input annotation file is missing required columns, needed columns:
......
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