R/app-BamBoozle.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

###################################################################
# Functional Genomics Center Zurich
# This code is distributed under the terms of the GNU General
# Public License Version 3, June 2007.
# The terms are available here: http://www.gnu.org/licenses/gpl.html
# www.fgcz.ch
###################################################################

##' @template app-template
##' @templateVar method ezMethodBamBoozle(input=NA, output=NA, param=NA)
##' @description Use this reference class to run 
EzAppBamBoozle <-
    setRefClass("EzAppBamBoozle",
                contains = "EzApp",
                methods = list(
                    initialize = function()
                    {
                        "Initializes the application using its specific defaults."
                        runMethod <<- ezMethodBamBoozle
                        name <<- "EzAppBamBoozle"
                    }
                )
    )

ezMethodBamBoozle = function(input=NA, output=NA, param=NA){
    bamFile = input$getFullPaths("BAM")
    file.copy(bamFile, basename(bamFile))
    genomeFa = param$ezRef["refFastaFile"]
    outFile <- sub('.bam', '_cleaned.bam', basename(bamFile))
    
    cmd <- paste('BAMboozle --bam', basename(bamFile), '--fa', genomeFa, '--out', outFile, '--p', param$cores, param$cmdOptions)
    ezSystem(cmd)
    
    fq1 <- sub('.bam', '_R1.fastq', outFile)
    if(param$paired){
        system(paste('samtools sort -n', outFile, '-@', param$cores, '-o sortedBam.bam'))
        fq2 <- sub('.bam', '_R2.fastq', outFile)
        cmd <- paste('bedtools bamtofastq -i sortedBam.bam', '-fq', fq1, '-fq2' , fq2)
    } else {
        fq2 <- ''
        cmd <- paste('bedtools bamtofastq -i', outFile, '-fq', fq1)
    }
    system(cmd)
    system(paste('pigz --best -p', param$cores, fq1, fq2))
    return('suceess')
}