Nothing

```
library(bcSeq)
#devtools::load_all("../")
#### Set the seed
set.seed(4523)
#### Generate barcode
lFName <- "./libFile.fasta"
bases <- c(rep('A', 4), rep('C',4), rep('G',4), rep('T',4))
numOfBars <- 7
Barcodes <- rep(NA, numOfBars*2)
for (i in 1:numOfBars){
Barcodes[2*i-1] <- paste0(">barcode_ID: ", i)
Barcodes[2*i] <- paste(sample(bases, length(bases)), collapse = '')
}
write(Barcodes, lFName)
#### Generate reads and phred score
rFName <- "./readFile.fastq"
numOfReads <- 8
Reads <- rep(NA, numOfReads*4)
for (i in 1:numOfReads){
Reads[4*i-3] <- paste0("@read_ID_",i)
Reads[4*i-2] <- Barcodes[2*sample(1:numOfBars,1,
replace=TRUE, prob=seq(1:numOfBars))]
Reads[4*i-1] <- "+"
Reads[4*i] <- paste(rawToChar(as.raw(
33+sample(20:30, length(bases),replace=TRUE))),
collapse='')
}
write(Reads, rFName)
#### perform alignment
ReadFile <- "./readFile.fastq"
BarFile <- "./libFile.fasta"
outFile <- "./countH.csv"
#### with default output for bcSeq_hamming
#res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
# tMat = NULL, numThread = 2, count_only = TRUE )
#res <- read.csv(outFile, header=FALSE)
#res
#### with return of alignment probability matrix to R
#outFile <- "./countH2.csv"
#res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
# tMat = NULL, numThread = 2, count_only = FALSE )
#res
#### with default output for bcSeq_edit
outFile <- "./countE.csv"
#res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
# tMat = NULL, numThread = 2, count_only = TRUE,
# gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
# pen_max = 7)
#res <- read.csv(outFile, header=FALSE)
#res
#### with return of alignment probability matrix to R
#outFile <- "./countE2.csv"
#res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
# tMat = NULL, numThread = 2, count_only = FALSE,
# gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
# pen_max = 7)
#res
#### user-defined probability model
comstomizeP <- function(m, x, y)
{
x * (1 - log(2) + log(1 + m / (m + y) ) )
}
outFile = "comstomizeP.csv"
#bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
# tMat = NULL, numThread = 2, count_only = TRUE,
# gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
# pen_max = 7, userProb = comstomizeP)
```

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