Fix missing name refactorings

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

@@ -265,8 +265,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
 
   def summaryStats: Map[String, Any] = {
     if (statsText) {
-      val stats_file: File = new File(output.getAbsolutePath + "_summary.txt")
-      parseStatsFile(stats_file)
+      val statsFile: File = new File(output.getAbsolutePath + "_summary.txt")
+      parseStatsFile(statsFile)
     } else {
       Map()
     }

public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala

@@ -102,85 +102,45 @@ class VcfFilterTest extends TestNGSuite with Matchers {
     val command = cmd(vcfFilter.cmdLine)
 
     var cmdString: List[String] = Nil
-    if (minSampleDepth.isDefined) {
-      cmdString = "--minSampleDepth " + minSampleDepth.getOrElse("") :: cmdString
-    }
+    if (minSampleDepth.isDefined) cmdString = "--minSampleDepth " + minSampleDepth.getOrElse("") :: cmdString
 
-    if (minTotalDepth.isDefined) {
-      cmdString = "--minTotalDepth " + minTotalDepth.getOrElse("") :: cmdString
-    }
+    if (minTotalDepth.isDefined) cmdString = "--minTotalDepth " + minTotalDepth.getOrElse("") :: cmdString
 
-    if (minAlternateDepth.isDefined) {
-      cmdString = "--minAlternateDepth " + minAlternateDepth.getOrElse("") :: cmdString
-    }
+    if (minAlternateDepth.isDefined) cmdString = "--minAlternateDepth " + minAlternateDepth.getOrElse("") :: cmdString
 
-    if (minSamplesPass.isDefined) {
-      cmdString = "--minSamplesPass " + minSamplesPass.getOrElse("") :: cmdString
-    }
+    if (minSamplesPass.isDefined) cmdString = "--minSamplesPass " + minSamplesPass.getOrElse("") :: cmdString
 
-    if (minGenomeQuality.isDefined) {
-      cmdString = "--minGenomeQuality " + minGenomeQuality.getOrElse("") :: cmdString
-    }
+    if (minGenomeQuality.isDefined) cmdString = "--minGenomeQuality " + minGenomeQuality.getOrElse("") :: cmdString
 
-    if (filterRefCalls) {
-      cmdString = "--filterRefCalls" :: cmdString
-    }
+    if (filterRefCalls) cmdString = "--filterRefCalls" :: cmdString
 
-    if (invertedOutputVcf.isDefined) {
-      cmdString = "--invertedOutputVcf " + invertedOutputVcf.getOrElse(new File("")).getAbsolutePath :: cmdString
-    }
+    if (invertedOutputVcf.isDefined) cmdString = "--invertedOutputVcf " + invertedOutputVcf.getOrElse(new File("")).getAbsolutePath :: cmdString
 
-    if (resToDom.isDefined) {
-      cmdString = "--resToDom " + resToDom.getOrElse("") :: cmdString
-    }
+    if (resToDom.isDefined) cmdString = "--resToDom " + resToDom.getOrElse("") :: cmdString
 
-    if (trioCompound.isDefined) {
-      cmdString = "--trioCompound " + trioCompound.getOrElse("") :: cmdString
-    }
+    if (trioCompound.isDefined) cmdString = "--trioCompound " + trioCompound.getOrElse("") :: cmdString
 
-    if (deNovoInSample.isDefined) {
-      cmdString = "--deNovoInSample " + deNovoInSample.getOrElse("") :: cmdString
-    }
+    if (deNovoInSample.isDefined) cmdString = "--deNovoInSample " + deNovoInSample.getOrElse("") :: cmdString
 
-    if (deNovoTrio.isDefined) {
-      cmdString = "--deNovoTrio " + deNovoTrio.getOrElse("") :: cmdString
-    }
+    if (deNovoTrio.isDefined) cmdString = "--deNovoTrio " + deNovoTrio.getOrElse("") :: cmdString
 
-    if (trioLossOfHet.isDefined) {
-      cmdString = "--trioLossOfHet " + trioLossOfHet.getOrElse("") :: cmdString
-    }
+    if (trioLossOfHet.isDefined) cmdString = "--trioLossOfHet " + trioLossOfHet.getOrElse("") :: cmdString
 
-    if (mustHaveVariant.nonEmpty) {
-      cmdString = mustHaveVariant.map(x => "--mustHaveVariant " + x) ::: cmdString
-    }
+    if (mustHaveVariant.nonEmpty) cmdString = mustHaveVariant.map(x => "--mustHaveVariant " + x) ::: cmdString
 
-    if (calledIn.nonEmpty) {
-      cmdString = calledIn.map(x => "--calledIn " + x) ::: cmdString
-    }
+    if (calledIn.nonEmpty) cmdString = calledIn.map(x => "--calledIn " + x) ::: cmdString
 
-    if (mustHaveGenotype.nonEmpty) {
-      cmdString = mustHaveGenotype.map(x => "--mustHaveGenotype " + x) ::: cmdString
-    }
+    if (mustHaveGenotype.nonEmpty) cmdString = mustHaveGenotype.map(x => "--mustHaveGenotype " + x) ::: cmdString
 
-    if (diffGenotype.nonEmpty) {
-      cmdString = diffGenotype.map(x => "--diffGenotype " + x) ::: cmdString
-    }
+    if (diffGenotype.nonEmpty) cmdString = diffGenotype.map(x => "--diffGenotype " + x) ::: cmdString
 
-    if (filterHetVarToHomVar.nonEmpty) {
-      cmdString = filterHetVarToHomVar.map(x => "--filterHetVarToHomVar " + x) ::: cmdString
-    }
+    if (filterHetVarToHomVar.nonEmpty) cmdString = filterHetVarToHomVar.map(x => "--filterHetVarToHomVar " + x) ::: cmdString
 
-    if (id.nonEmpty) {
-      cmdString = id.map(x => "--id " + x) ::: cmdString
-    }
+    if (id.nonEmpty) cmdString = id.map(x => "--id " + x) ::: cmdString
 
-    if (idFile.isDefined) {
-      cmdString = "--idFile " + idFile.getOrElse(new File("")).getAbsolutePath :: cmdString
-    }
+    if (idFile.isDefined) cmdString = "--idFile " + idFile.getOrElse(new File("")).getAbsolutePath :: cmdString
 
-    if (minQualScore.isDefined) {
-      cmdString = "--minQualScore " + minQualScore.getOrElse("") :: cmdString
-    }
+    if (minQualScore.isDefined) cmdString = "--minQualScore " + minQualScore.getOrElse("") :: cmdString
 
     cmdString.foreach(x => command.contains(x) shouldBe true)
   }

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala

@@ -34,25 +34,25 @@ class AnnotateVcfWithBedTest extends TestNGSuite with MockitoSugar with Matchers
     Paths.get(getClass.getResource(p).toURI).toString
   }
 
-  val vepped_path = resourcePath("/VEP_oneline.vcf")
+  val veppedPath = resourcePath("/VEP_oneline.vcf")
   val bed = resourcePath("/rrna01.bed")
   val rand = new Random()
 
   @Test def testOutputTypeVcf() = {
     val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf"
-    val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
+    val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath, "-B", bed, "-f", "testing")
     main(arguments)
   }
 
   @Test def testOutputTypeBcf() = {
     val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".bcf"
-    val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
+    val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath, "-B", bed, "-f", "testing")
     main(arguments)
   }
 
   @Test def testOutputTypeVcfGz() = {
     val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf.gz"
-    val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
+    val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath, "-B", bed, "-f", "testing")
     main(arguments)
   }
 

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala

@@ -37,7 +37,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
     Paths.get(getClass.getResource(p).toURI).toString
   }
 
-  val vepped_path = resourcePath("/chrQ.vcf.gz")
+  val veppedPath = resourcePath("/chrQ.vcf.gz")
   val reference = resourcePath("/fake_chrQ.fa")
 
   // These two have to created
@@ -52,7 +52,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
     val tmp = File.createTempFile("MergeAlleles", ".vcf")
     tmp.deleteOnExit()
     val tmpPath = tmp.getAbsolutePath
-    val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
+    val arguments = Array("-I", veppedPath, "-o", tmpPath, "-R", reference)
     main(arguments)
   }
 
@@ -60,7 +60,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
     val tmp = File.createTempFile("MergeAlleles", ".vcf.gz")
     tmp.deleteOnExit()
     val tmpPath = tmp.getAbsolutePath
-    val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
+    val arguments = Array("-I", veppedPath, "-o", tmpPath, "-R", reference)
     main(arguments)
   }
 
@@ -68,7 +68,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
     val tmp = File.createTempFile("MergeAlleles", ".bcf")
     tmp.deleteOnExit()
     val tmpPath = tmp.getAbsolutePath
-    val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
+    val arguments = Array("-I", veppedPath, "-o", tmpPath, "-R", reference)
     main(arguments)
   }
 }

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala

@@ -39,31 +39,31 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
     Paths.get(getClass.getResource(p).toURI).toString
   }
 
-  val vepped_path = resourcePath("/VEP_oneline.vcf")
-  val vepped = new File(vepped_path)
+  val veppedPath = resourcePath("/VEP_oneline.vcf")
+  val vepped = new File(veppedPath)
   val rand = new Random()
 
   @Test def testOutputTypeVcf() = {
     val tmp = File.createTempFile("VcfFilter", ".vcf")
     tmp.deleteOnExit()
-    val tmp_path = tmp.getAbsolutePath
-    val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+    val tmpPath = tmp.getAbsolutePath
+    val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath)
     main(arguments)
   }
 
   @Test def testOutputTypeBcf() = {
     val tmp = File.createTempFile("VcfFilter", ".bcf")
     tmp.deleteOnExit()
-    val tmp_path = tmp.getAbsolutePath
-    val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+    val tmpPath = tmp.getAbsolutePath
+    val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath)
     main(arguments)
   }
 
   @Test def testOutputTypeVcfGz() = {
     val tmp = File.createTempFile("VcfFilter", ".vcf.gz")
     tmp.deleteOnExit()
-    val tmp_path = tmp.getAbsolutePath
-    val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+    val tmpPath = tmp.getAbsolutePath
+    val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath)
     main(arguments)
   }
 
@@ -73,22 +73,22 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
      */
     val tmp = File.createTempFile("VCfFilter", ".vcf.gz")
     tmp.deleteOnExit()
-    val tmp_path = tmp.getAbsolutePath
-    val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path,
+    val tmpPath = tmp.getAbsolutePath
+    val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath,
       "--mustHaveGenotype", "Sample_101:HET")
     main(arguments)
 
-    val size = new VCFFileReader(new File(tmp_path), false).size
+    val size = new VCFFileReader(new File(tmpPath), false).size
     size shouldBe 1
 
     val tmp2 = File.createTempFile("VcfFilter", ".vcf.gz")
     tmp2.deleteOnExit()
-    val tmp2_path = tmp2.getAbsolutePath
-    val arguments2: Array[String] = Array("-I", vepped_path, "-o", tmp2_path,
+    val tmpPath2 = tmp2.getAbsolutePath
+    val arguments2: Array[String] = Array("-I", veppedPath, "-o", tmpPath2,
       "--mustHaveGenotype", "Sample_101:HOM_VAR")
     main(arguments2)
 
-    val size2 = new VCFFileReader(new File(tmp2_path), false).size
+    val size2 = new VCFFileReader(new File(tmpPath2), false).size
     size2 shouldBe 0
 
   }

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -31,7 +31,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   var inputR1: File = _
 
   @Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", required = false)
-  var input_R2: Option[File] = None
+  var inputR2: Option[File] = None
 
   /** Skip Trim fastq files */
   var skipTrim: Boolean = config("skip_trim", default = false)
@@ -48,13 +48,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   /** Returns files to store in summary */
   def summaryFiles: Map[String, File] = {
     Map("input_R1" -> inputR1, "output_R1" -> fastqR1Qc) ++
-      (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> fastqR2Qc.get) else Map())
+      (if (paired) Map("input_R2" -> inputR2.get, "output_R2" -> fastqR2Qc.get) else Map())
   }
 
   /** returns settings to store in summary */
   def summarySettings = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip, "paired" -> paired)
 
-  var paired: Boolean = input_R2.isDefined
+  var paired: Boolean = inputR2.isDefined
   var R1Name: String = _
   var R2Name: String = _
 
@@ -80,13 +80,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     require(sampleId != null, "Missing sample ID on flexiprep module")
     require(libId != null, "Missing library ID on flexiprep module")
 
-    paired = input_R2.isDefined
+    paired = inputR2.isDefined
 
     inputFiles :+= new InputFile(inputR1)
-    input_R2.foreach(inputFiles :+= new InputFile(_))
+    inputR2.foreach(inputFiles :+= new InputFile(_))
 
     R1Name = getUncompressedFileName(inputR1)
-    input_R2.foreach { fileR2 =>
+    inputR2.foreach { fileR2 =>
       paired = true
       R2Name = getUncompressedFileName(fileR2)
     }
@@ -96,7 +96,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   def biopetScript() {
     runInitialJobs()
 
-    if (paired) runTrimClip(inputR1, input_R2, outputDir)
+    if (paired) runTrimClip(inputR1, inputR2, outputDir)
     else runTrimClip(inputR1, outputDir)
 
     val R1Files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
@@ -107,7 +107,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   /** Add init non chunkable jobs */
   def runInitialJobs() {
     outputFiles += ("fastq_input_R1" -> inputR1)
-    if (paired) outputFiles += ("fastq_input_R2" -> input_R2.get)
+    if (paired) outputFiles += ("fastq_input_R2" -> inputR2.get)
 
     fastqcR1 = Fastqc(this, inputR1, new File(outputDir, R1Name + ".fastqc/"))
     add(fastqcR1)
@@ -116,7 +116,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
     val validateFastq = new ValidateFastq(this)
     validateFastq.r1Fastq = inputR1
-    validateFastq.r2Fastq = input_R2
+    validateFastq.r2Fastq = inputR2
     validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.log.out")
     add(validateFastq)
 
@@ -128,7 +128,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     }
 
     if (paired) {
-      fastqcR2 = Fastqc(this, input_R2.get, new File(outputDir, R2Name + ".fastqc/"))
+      fastqcR2 = Fastqc(this, inputR2.get, new File(outputDir, R2Name + ".fastqc/"))
       add(fastqcR2)
       addSummarizable(fastqcR2, "fastqc_R2")
       outputFiles += ("fastqc_R2" -> fastqcR2.output)
@@ -140,7 +140,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     addSummarizable(seqstatR1, "seqstat_R1")
 
     if (paired) {
-      val seqstatR2 = SeqStat(this, input_R2.get, outputDir)
+      val seqstatR2 = SeqStat(this, inputR2.get, outputDir)
       seqstatR2.isIntermediate = true
       add(seqstatR2)
       addSummarizable(seqstatR2, "seqstat_R2")

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -71,7 +71,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
     val flexiprep: Flexiprep = initPipeline(map)
 
     flexiprep.inputR1 = (if (zipped) FlexiprepTest.r1Zipped else FlexiprepTest.r1)
-    if (paired) flexiprep.input_R2 = Some((if (zipped) FlexiprepTest.r2Zipped else FlexiprepTest.r2))
+    if (paired) flexiprep.inputR2 = Some((if (zipped) FlexiprepTest.r2Zipped else FlexiprepTest.r2))
     flexiprep.sampleId = Some("1")
     flexiprep.libId = Some("1")
     flexiprep.script()

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala

@@ -98,7 +98,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
       flexiprep.sampleId = Some(sampleId)
       flexiprep.libId = Some(libId)
       flexiprep.inputR1 = config("R1")
-      flexiprep.input_R2 = config("R2")
+      flexiprep.inputR2 = config("R2")
       flexiprep.outputDir = new File(libDir, "flexiprep")
 
       lazy val gs = new GearsSingle(qscript)
@@ -109,7 +109,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
       /** Function that add library jobs */
       protected def addJobs(): Unit = {
         inputFiles :+= InputFile(flexiprep.inputR1, config("R1_md5"))
-        flexiprep.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
+        flexiprep.inputR2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
         add(flexiprep)
 
         gs.fastqR1 = Some(flexiprep.fastqR1Qc)

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

@@ -80,7 +80,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
     if (!skipFlexiprep) {
       val flexiprep = new Flexiprep(this)
       flexiprep.inputR1 = r1
-      flexiprep.input_R2 = r2
+      flexiprep.inputR2 = r2
       flexiprep.outputDir = new File(outputDir, "flexiprep")
       add(flexiprep)
       (flexiprep.fastqR1Qc, flexiprep.fastqR2Qc)

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -167,7 +167,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     if (!skipFlexiprep) {
       flexiprep.outputDir = new File(outputDir, "flexiprep")
       flexiprep.inputR1 = inputR1
-      flexiprep.input_R2 = inputR2
+      flexiprep.inputR2 = inputR2
       flexiprep.sampleId = this.sampleId
       flexiprep.libId = this.libId
       flexiprep.init()
@@ -184,7 +184,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
           if (paired) Some(new File(chunkDir, inputR2.get.getName)) else None)
       }).toMap
       else if (skipFlexiprep) Map(outputDir -> (inputR1, if (paired) inputR2 else None))
-      else Map(outputDir -> (flexiprep.inputR1, flexiprep.input_R2))
+      else Map(outputDir -> (flexiprep.inputR1, flexiprep.inputR2))
     }
 
     if (chunking) {