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

This reverts commit 2b618795.

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala

-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")
-}