lavToPsl {CNEr} | R Documentation

## lavToPsl

### Description

Wrapper function of `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

`lavs` | `character`(n): file names of input lav files.
`psls` | codecharacter(n): file names of output psl files. By default, in the same folder of input lav files with same names.
`removeLav` | `boolean`: When `TRUE`, the input lavs files will be removed after the conversion.
`binary` | `character`(1): the name/filename of the binary `lavToPsl` to call.

### Value

`character`(n): the file names of output psl files.

### Author(s)

Ge Tan

### References

http://hgdownload.cse.ucsc.edu/admin/exe/

### See Also

`lastz`

### Examples

      ## Not run:
      ## 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")

    ## End(Not run)

[Package CNEr version 1.20.0 Index]