HardFilter.scala

package org.broadinstitute.sting.queue.qscripts

import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._

class HardFilter extends QScript {
    // Create an alias 'qscript' to be able to access variables in the HardFilter.
    // 'qscript' is now the same as 'HardFilter.this'
    qscript =>

    // Required arguments.  All initialized to empty values.
    @Input(doc="The reference file", shortName="R", required=true)
    var referenceFile: File = _

    @Input(doc="Raw vcf file", shortName="V")
    var rawVCF: File =_

    @Input(doc="Output core filename.", shortName="O", required=true)
    var out: File = _

    @Argument(doc="Maximum amount of memory", shortName="mem", required=true)
    var maxMem: Int = _

    @Argument(doc="Number of scatters", shortName="nsc", required=true)
    var numScatters: Int = _

    // filteroptions
    @Argument(doc="Filter mode: BOTH, SNP or INDEL", shortName="mode", required=true)
    var filterMode: String = _
    
    @Argument(doc="A optional list of SNPfilter names.", shortName="snpFilterName", required=false)
    var snpFilterNames: List[String] = _
  
    @Argument(doc="An optional list of filter expressions.", shortName="snpFilterExpression", required=false)
    var snpFilterExp: List[String] = _
    
    @Argument(doc="An optional list of INDEL filter names.", shortName="indelFilterName", required=false)
    var indelFilterNames: List[String] = _
      
    @Argument(doc="An optional list of INDEL filter expressions.", shortName="indelFilterExpression", required=false)
    var indelFilterExp: List[String] = _
    
    @Argument(doc="The number of SNPs which make up a cluster.", shortName="cluster", required=false)
    var clusterSize: Int = 0
    
    @Argument(doc="The window size (in bases) in which to evaluate clustered SNPs.", shortName="window", required=false)
    var clusterWindowSize: Int = 0

    // This trait allows us set the variables below in one place and then reuse this trait on each CommandLineGATK function below.
    trait HF_Arguments extends CommandLineGATK {
	this.reference_sequence = referenceFile
	this.memoryLimit = maxMem
    }

    def script() {
	val selectSNP = new SelectVariants with HF_Arguments
	selectSNP.V = rawVCF
	selectSNP.selectType :+= org.broadinstitute.variant.variantcontext.VariantContext.Type.SNP
	selectSNP.selectType :+= org.broadinstitute.variant.variantcontext.VariantContext.Type.NO_VARIATION
	selectSNP.out = qscript.out + ".raw_snps.vcf"

	val SNPfilter = new VariantFiltration with HF_Arguments
	SNPfilter.scatterCount = numScatters
	SNPfilter.V = rawVCF
	SNPfilter.out = qscript.out + ".filtered_snps.vcf"
	SNPfilter.filterExpression = snpFilterExp 
	SNPfilter.filterName = snpFilterNames
	
	if( clusterSize != 0 && clusterWindowSize != 0 ){
	    SNPfilter.clusterSize = clusterSize
	    SNPfilter.clusterWindowSize = clusterWindowSize
	}

	val selectINDEL = new SelectVariants with HF_Arguments
	selectINDEL.V = rawVCF
	selectINDEL.selectType :+= org.broadinstitute.variant.variantcontext.VariantContext.Type.INDEL
	selectINDEL.out = qscript.out + ".raw_indels.vcf"

	val INDELfilter = new VariantFiltration with HF_Arguments
	INDELfilter.scatterCount = numScatters
	INDELfilter.V = rawVCF
	INDELfilter.out = qscript.out + ".filtered_indels.vcf"
	INDELfilter.filterExpression = indelFilterExp
	INDELfilter.filterName = indelFilterNames

	val CombineVars = new CombineVariants with HF_Arguments
	CombineVars.V :+= SNPfilter.out
	CombineVars.V :+= INDELfilter.out
	CombineVars.out = qscript.out + ".filtered_variants.vcf"

	if (filterMode == "SNP" || filterMode == "BOTH") { add(selectSNP, SNPfilter) }
	if (filterMode == "INDEL" || filterMode == "BOTH") { add(selectINDEL, INDELfilter) }
	if (filterMode == "BOTH") { add(CombineVars) }
     }
}