lastz wrapper

Description

Wrapper function of lastz to do the pairwise whole genome alignment. This function doesn't work on Windows platform.

Usage

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  lastz(assemblyTarget, assemblyQuery, outputDir = ".",
        chrsTarget = NULL, chrsQuery = NULL,
        distance = c("far", "medium", "near"), binary = "lastz", 
        mc.cores = getOption("mc.cores", 2L), echoCommand = FALSE)

Arguments

assemblyTarget

character(1): the file name of target assembly twoBit file.

assemblyQuery

character(1): the file name of query assembly twoBit file.

outputDir

character(1): the folder to put the generated lav files.

chrsTarget

NULL or character(n): when it's NULL, all the available chromosomes from the target assembly will be aligned.

chrsQuery

NULL or character(n): when it's NULL, all the available chromosomes from the query assembly will be aligned.

distance

It can be "far", "medium" or "near". It decides the score matrix used in lastz aligner. See '?scoringMatrix' for more details.

binary

character(1): the name/filename of the binary lastz to call.

mc.cores

integer(1): the number of threads to use. By default, getOption("mc.cores", 2L).

echoCommand

boolean(1): When TRUE, only the command to run lastz is returned.

Value

A character(n) vector of ouput lav file names.

Note

lastz aligner must be installed on the machine to use this function.

Author(s)

Ge Tan

References

http://www.bx.psu.edu/~rsharris/lastz/

See Also

lavToPsl

Examples

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  ## Not run: 
  ## This example doesn't run because it requires two bit files and external
  ## Kent utilities.
    assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
    assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
    lavs <- lastz(assemblyTarget, assemblyQuery, 
                  outputDir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
			            chrsTarget=c("chr1", "chr2", "chr3"),
			            chrsQuery=c("chr1", "chr2", "chr3"),
			            distance="far", mc.cores=4)
  
## End(Not run)

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