# READ GATK files ============================
setdec <- function(lines) {
res = "."
if (length(grep(",", lines)) > 0) {
res=","
}
res
}
hs_metrics = function(infile){
lines <- readLines(infile)
dec = setdec(lines[7:8])
metrics <- rbind(read.table(textConnection(lines[7:8]), header=TRUE, fill=TRUE, sep="\t", na.strings=c("?"), dec=dec))
as.data.frame(metrics, stringsAsFactors=F)
}
get_hs_metrics <- function(folder, sname="E") {
f = list.files(folder, "hs_metrics", full.names = T)
n = list.files(folder, "hs_metrics", full.names = F)
n = gsub(".hs_metrics.txt","",n)
names(f)=n
f =f[grep(sname, f)]
hs =lapply(f, hs_metrics);
hs = do.call(rbind, hs)
# hs$SAMPLE=rownames(hs)
# hs$LIBRARY=date
hs
}
get_targeted_metrics <- function(folder, sname="E") {
f = list.files(folder, "targeted_metrics", full.names = T)
n = list.files(folder, "targeted_metrics", full.names = F)
n = gsub(".targeted_metrics.txt","",n)
names(f)=n
f =f[grep(sname, f)]
hs =lapply(f, hs_metrics);
hs = do.call(rbind, hs)
# hs$SAMPLE=rownames(hs)
# hs$LIBRARY=date
hs
}
get_coverage = function(folder, sname="E"){
f = list.files(folder, "coverage", full.names = T)
n = list.files(folder, "coverage", full.names = F)
n = gsub(".coverage.txt","",n)
names(f) = n
f =f[grep(sname, f)]
hs =lapply(f, read.delim)#;names(hs) =n
hs
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.