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\name{lavToPsl}
\alias{lavToPsl}
\title{
lavToPsl
}
\description{
Wrapper function of \command{lavToPsl}: Convert blastz lav to psl format.
This function doesn't work on Windows platform since Kent utilities only
support Linux and Unix platforms.
}
\usage{
lavToPsl(lavs, psls=sub("\\\.lav$", ".psl", lavs, ignore.case = TRUE),
removeLav=TRUE, binary="lavToPsl")
}
\arguments{
\item{lavs}{
\code{character}(n): file names of input \emph{lav} files.
}
\item{psls}{
code{character}(n): file names of output \emph{psl} files.
By default, in the same folder of input lav files with same names.
}
\item{removeLav}{
\code{boolean}: When \code{TRUE}, the input \emph{lavs} files will be
removed after the conversion.
}
\item{binary}{
\code{character}(1): the name/filename of the binary \command{lavToPsl}
to call.
}
}
\value{
\code{character}(n): the file names of output \emph{psl} files.
}
\references{
\url{http://hgdownload.cse.ucsc.edu/admin/exe/}
}
\author{
Ge Tan
}
\seealso{
\code{\link{lastz}}
}
\examples{
\dontrun{
## This example doesn't run because it requires lav files from previous steps
## and external Kent utilities.
lavs <- tools::list_files_with_exts(
dir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt", exts="lav")
lavToPsl(lavs, removeLav=FALSE, binary="lavToPsl")
}
}
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