Commit bba51033 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Revert "PindelVCF wrapper", does not belong to this branch

This reverts commit 2b618795.
parent 2b618795
package nl.lumc.sasc.biopet.extensions.pindel
import java.io.File
import nl.lumc.sasc.biopet.core.{ Version, Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by wyleung on 20-1-16.
*/
class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
executable = config("exe", default = "pindel2vcf")
override def defaultCoreMemory = 2.0
override def defaultThreads = 1
def versionRegex = """Version:? (.*)""".r
override def versionExitcode = List(1)
def versionCommand = executable + " -h"
/**
* Required parameters
*/
@Input
var reference: File = referenceFasta
@Output
var outputVCF: File = _
var referenceDate: String = config("reference_date")
override def beforeGraph: Unit = {
if (reference == null) reference = referenceFasta()
}
var pindelOutput: Option[File] = config("pindel_output")
var pindelOutputRoot: Option[File] = config("pindel_output_root")
var chromosome: Option[String] = config("chromosome")
var windowSize: Option[Int] = config("window_size")
var minCoverage: Option[Int] = config("min_coverage")
var hetCutoff: Option[Float] = config("het_cutoff")
var homCutoff: Option[Float] = config("hom_cutoff")
var minSize: Option[Int] = config("min_size")
var maxSize: Option[Int] = config("max_size")
var bothStrandSupported: Boolean = config("both_strand_supported", default = false)
var minSupportingSamples: Option[Int] = config("min_supporting_samples")
var minSupportingReads: Option[Int] = config("min_supporting_reads")
var maxSupportingReads: Option[Int] = config("max_supporting_reads")
var regionStart: Option[Int] = config("region_start")
var regionEnd: Option[Int] = config("region_end")
var maxInternalRepeats: Option[Int] = config("max_internal_repeats")
var compactOutLimit: Option[Int] = config("compact_output_limit")
var maxInternalRepeatLength: Option[Int] = config("max_internal_repeatlength")
var maxPostindelRepeats: Option[Int] = config("max_postindel_repeat")
var maxPostindelRepeatLength: Option[Int] = config("max_postindel_repeatlength")
var onlyBalancedSamples: Boolean = config("only_balanced_samples")
var somaticP: Boolean = config("somatic_p")
var minimumStrandSupport: Option[Int] = config("minimum_strand_support")
var gatkCompatible: Boolean = config("gatk_compatible")
def cmdLine = required(executable) +
required("--reference_name", referenceSpecies) +
required("--reference_date", referenceDate) +
optional("--pindel_output", pindelOutput) +
optional("--pindel_output_root", pindelOutputRoot) +
required("--vcf", outputVCF) +
optional("--chromosome", chromosome) +
optional("--window_size", windowSize) +
optional("--min_coverage", minCoverage) +
optional("--het_cutoff", hetCutoff) +
optional("--hom_cutoff", homCutoff) +
optional("--min_size", minSize) +
optional("--max_size", maxSize) +
conditional(bothStrandSupported, "--both_strands_supported") +
optional("--min_supporting_samples", minSupportingSamples) +
optional("--min_supporting_reads", minSupportingReads) +
optional("--max_supporting_reads", maxSupportingReads) +
optional("--region_start", regionStart) +
optional("--region_end", regionEnd) +
optional("--max_internal_repeats", maxInternalRepeats) +
optional("--compact_output_limit", compactOutLimit) +
optional("--max_internal_repeatlength", maxInternalRepeatLength) +
optional("--max_postindel_repeats", maxPostindelRepeats) +
optional("--max_postindel_repeatlength", maxPostindelRepeatLength) +
conditional(onlyBalancedSamples, "--only_balanced_samples") +
conditional(somaticP, "--somatic_p") +
optional("--minimum_strand_support", minimumStrandSupport) +
conditional(gatkCompatible, "--gatk_compatible")
}
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