Remove unused code

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -40,17 +40,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   var useAllelesOption: Boolean = config("use_alleles_option", default = false)
   val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
 
-  /**
-   * class LibraryOutput extends AbstractLibraryOutput {
-   * var mappedBamFile: File = _
-   * var variantcalling: GatkVariantcalling.ScriptOutput = _
-   * }
-   *
-   * class SampleOutput extends AbstractSampleOutput {
-   * var variantcalling: GatkVariantcalling.ScriptOutput = _
-   * }
-   */
-
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
     def makeLibrary(id: String) = new Library(id)
@@ -217,131 +206,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
       }
     }
   }
-
-  /*
-  // Called for each sample
-  def runSingleSampleJobs(sampleID: String): SampleOutput = {
-    val sampleOutput = new SampleOutput
-    var libraryBamfiles: List[File] = List()
-    sampleOutput.libraries = runLibraryJobs(sampleID)
-    val sampleDir = globalSampleDir + sampleID
-    for ((libraryID, libraryOutput) <- sampleOutput.libraries) {
-      libraryBamfiles ++= libraryOutput.variantcalling.bamFiles
-    }
-
-    if (libraryBamfiles.size > 0) {
-      finalBamFiles ++= libraryBamfiles
-      val gatkVariantcalling = new GatkVariantcalling(this)
-      gatkVariantcalling.inputBams = libraryBamfiles
-      gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
-      gatkVariantcalling.preProcesBams = false
-      if (!singleSampleCalling) {
-        gatkVariantcalling.useHaplotypecaller = false
-        gatkVariantcalling.useUnifiedGenotyper = false
-      }
-      gatkVariantcalling.sampleID = sampleID
-      gatkVariantcalling.init
-      gatkVariantcalling.biopetScript
-      addAll(gatkVariantcalling.functions)
-      sampleOutput.variantcalling = gatkVariantcalling.scriptOutput
-      gvcfFiles :+= gatkVariantcalling.scriptOutput.gvcfFile
-    } else logger.warn("No bamfiles for variant calling for sample: " + sampleID)
-    return sampleOutput
-  }
-
-  // Called for each run from a sample
-  def runSingleLibraryJobs(libraryId: String, sampleID: String): LibraryOutput = {
-    val libraryOutput = new LibraryOutput
-    val runDir: String = globalSampleDir + sampleID + "/run_" + libraryId + "/"
-    var inputType: String = config("inputtype", default = "dna")
-
-    def loadFromLibraryConfig(startJobs: Boolean = true): Mapping = {
-      val mapping = new Mapping(this)
-
-      mapping.input_R1 = config("R1")
-      mapping.input_R2 = config("R2")
-      mapping.RGLB = libraryId
-      mapping.RGSM = sampleID
-      mapping.RGPL = config("PL")
-      mapping.RGPU = config("PU")
-      mapping.RGCN = config("CN")
-      mapping.outputDir = runDir
-
-      if (startJobs) {
-        mapping.init
-        mapping.biopetScript
-      }
-      return mapping
-    }
-
-    if (config.contains("R1")) {
-      val mapping = loadFromLibraryConfig()
-      addAll(mapping.functions) // Add functions of mapping to curent function pool
-      libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
-    } else if (config.contains("bam")) {
-      var bamFile: File = config("bam")
-      if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile)
-
-      if (config("bam_to_fastq", default = false).asBoolean) {
-        val samToFastq = SamToFastq(this, bamFile, runDir + sampleID + "-" + libraryId + ".R1.fastq",
-          runDir + sampleID + "-" + libraryId + ".R2.fastq")
-        add(samToFastq, isIntermediate = true)
-        val mapping = loadFromLibraryConfig(startJobs = false)
-        mapping.input_R1 = samToFastq.fastqR1
-        mapping.input_R2 = samToFastq.fastqR2
-        mapping.init
-        mapping.biopetScript
-        addAll(mapping.functions) // Add functions of mapping to curent function pool
-        libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
-      } else {
-        var readGroupOke = true
-        val inputSam = SamReaderFactory.makeDefault.open(bamFile)
-        val header = inputSam.getFileHeader.getReadGroups
-        for (readGroup <- inputSam.getFileHeader.getReadGroups) {
-          if (readGroup.getSample != sampleID) logger.warn("Sample ID readgroup in bam file is not the same")
-          if (readGroup.getLibrary != libraryId) logger.warn("Library ID readgroup in bam file is not the same")
-          if (readGroup.getSample != sampleID || readGroup.getLibrary != libraryId) readGroupOke = false
-        }
-        inputSam.close
-
-        if (!readGroupOke) {
-          if (config("correct_readgroups", default = false)) {
-            logger.info("Correcting readgroups, file:" + bamFile)
-            val aorrg = AddOrReplaceReadGroups(this, bamFile, new File(runDir + sampleID + "-" + libraryId + ".bam"))
-            aorrg.RGID = sampleID + "-" + libraryId
-            aorrg.RGLB = libraryId
-            aorrg.RGSM = sampleID
-            aorrg.RGPL = config("PL", default = "illumina")
-            aorrg.RGPU = config("PU", default = "na")
-            aorrg.RGCN = config("CN")
-            add(aorrg, isIntermediate = true)
-            bamFile = aorrg.output
-          } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
-            "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
-        }
-        addAll(BamMetrics(this, bamFile, runDir + "metrics/").functions)
-
-        libraryOutput.mappedBamFile = bamFile
-      }
-    } else {
-      logger.error("Sample: " + sampleID + ": No R1 found for run: " + libraryId)
-      return libraryOutput
-    }
-
-    val gatkVariantcalling = new GatkVariantcalling(this)
-    gatkVariantcalling.inputBams = List(libraryOutput.mappedBamFile)
-    gatkVariantcalling.outputDir = runDir
-    gatkVariantcalling.variantcalling = config("library_variantcalling", default = false)
-    gatkVariantcalling.preProcesBams = true
-    gatkVariantcalling.sampleID = sampleID
-    gatkVariantcalling.init
-    gatkVariantcalling.biopetScript
-    addAll(gatkVariantcalling.functions)
-    libraryOutput.variantcalling = gatkVariantcalling.scriptOutput
-
-    return libraryOutput
-  }
-  */
 }
 
 object GatkPipeline extends PipelineCommand