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\name{chainMergeSort}
\alias{chainMergeSort}
\title{
chainMergeSort
}
\description{
Wrapper function of \command{chainMergeSort}:
Combines sorted files into a larger sorted file.
This function doesn't work on Windows platform since Kent utilities only
support Linux and Unix platforms.
}
\usage{
chainMergeSort(chains, assemblyTarget, assemblyQuery,
allChain=paste0(sub("\\\.2bit$", "", basename(assemblyTarget),
ignore.case=TRUE), ".",
sub("\\\.2bit$", "", basename(assemblyQuery),
ignore.case=TRUE), ".all.chain"),
removeChains=TRUE, binary="chainMergeSort")
}
\arguments{
\item{chains}{
\code{character}(n): file names of input \emph{chains} files.
}
\item{assemblyTarget}{
\code{character}(1): the file name of target assembly \emph{twoBit} file.
}
\item{assemblyQuery}{
\code{character}(1): the file name of query assembly \emph{twoBit} file.
}
\item{allChain}{
\code{character}(1): file names of merged \emph{allChain} file.
}
\item{removeChains}{
\code{boolean}: When \code{TRUE}, the input \emph{chains} files will be
removed after the conversion.
}
\item{binary}{
\code{character}(1): the name/filename of the binary \command{chainMergeSort}
to call.
}
}
\details{
This \emph{allChain} file is what we get from UCSC download, \emph{e.g.},
\bold{hg19.danRer7.all.chain.gz}.
}
\value{
\code{character}(1): the file names of merged \emph{allChain} file.
}
\references{
\url{http://hgdownload.cse.ucsc.edu/admin/exe/}
}
\author{
Ge Tan
}
\seealso{
\code{\link{axtChain}}
}
\examples{
\dontrun{
## This example doesn't run because it requires two bit files and external
## Kent utilities.
chains <- tools::list_files_with_exts(
dir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt", exts="chain")
assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
chainMergeSort(chains, assemblyTarget, assemblyQuery,
allChain=file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
paste0(sub("\\\.2bit$", "", basename(assemblyTarget),
ignore.case=TRUE), ".",
sub("\\\.2bit$", "", basename(assemblyQuery),
ignore.case=TRUE), ".all.chain")),
removeChains=FALSE, binary="chainMergeSort")
}
}
|
