## need seqz file and sample name
args=commandArgs(T)
sample=args[1]
seqz=args[2]
out_prefix=args[3]
library("sequenza")
Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 1000)
#seqz.data <- read.seqz(CCW0032_small.seqz.gz)
#gc.stats <- gc.norm(x = seqz.data$depth.ratio,gc = seqz.data$GC.percent)
#gc.vect <- setNames(gc.stats$raw.mean, gc.stats$gc.values)
#seqz.data$adjusted.ratio <- seqz.data$depth.ratio/gc.vect[as.character(seqz.data$GC.percent)]

test <- sequenza.extract(args[2])
#names(test)
CP.example <- sequenza.fit(test)
sequenza.results(sequenza.extract = test, cp.table = CP.example,sample.id = args[1], out.dir=args[3])