Fixing compile and code warnings

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala

@@ -116,22 +116,22 @@ class VariantAnnotator(val parent: Configurable) extends CommandLineGATK with Sc
       outputIndex = VcfUtils.getVcfIndexFile(out)
   }
 
-  override def cmdLine = super.cmdLine +
-    required(TaggedFile.formatCommandLineParameter("-V", variant), variant, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-snpEffFile", snpEffFile.getOrElse()), snpEffFile, spaceSeparated = true, escape = true, format = "%s") +
-    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse()), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
-    repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
-    repeat("-resource", resource, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
-    optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
-    repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
-    repeat("-XA", excludeAnnotation, spaceSeparated = true, escape = true, format = "%s") +
-    repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
-    repeat("-E", expression, spaceSeparated = true, escape = true, format = "%s") +
-    conditional(resourceAlleleConcordance, "-rac", escape = true, format = "%s") +
-    conditional(useAllAnnotations, "-all", escape = true, format = "%s") +
-    conditional(alwaysAppendDbsnpId, "-alwaysAppendDbsnpId", escape = true, format = "%s") +
-    optional("-mvq", MendelViolationGenotypeQualityThreshold, spaceSeparated = true, escape = true, format = MendelViolationGenotypeQualityThresholdFormat) +
-    conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
-    conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
-    conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
+  override def cmdLine: String = super.cmdLine +
+    required(TaggedFile.formatCommandLineParameter("-V", variant), variant) +
+    optional(TaggedFile.formatCommandLineParameter("-snpEffFile", snpEffFile.getOrElse(new File("."))), snpEffFile) +
+    optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(new File("."))), dbsnp) +
+    repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter) +
+    repeat("-resource", resource, formatPrefix = TaggedFile.formatCommandLineParameter) +
+    optional("-o", out) +
+    repeat("-A", annotation) +
+    repeat("-XA", excludeAnnotation) +
+    repeat("-G", group) +
+    repeat("-E", expression) +
+    conditional(resourceAlleleConcordance, "-rac") +
+    conditional(useAllAnnotations, "-all") +
+    conditional(alwaysAppendDbsnpId, "-alwaysAppendDbsnpId") +
+    optional("-mvq", MendelViolationGenotypeQualityThreshold, format = MendelViolationGenotypeQualityThresholdFormat) +
+    conditional(filter_reads_with_N_cigar, "-filterRNC") +
+    conditional(filter_mismatching_base_and_quals, "-filterMBQ") +
+    conditional(filter_bases_not_stored, "-filterNoBases")
 }

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala

@@ -28,7 +28,7 @@ object Question {
     if (posibleValues.nonEmpty) println(s"possible values: ${posibleValues.mkString(", ")}")
     default.foreach(x => println(s"Default value: $x"))
     print(s"$name > ")
-    (Console.readLine.trim, default) match {
+    (scala.io.StdIn.readLine.trim, default) match {
       case (a, Some(d)) if a.isEmpty => d
       case (a, None) if a.isEmpty =>
         println("ERROR: Value is required")
@@ -50,7 +50,7 @@ object Question {
     description.foreach(println)
     default.foreach(x => println(s"Default value: $x"))
     print(s"$name (y/n) > ")
-    Console.readLine.trim.toLowerCase match {
+    scala.io.StdIn.readLine.trim.toLowerCase match {
       case "" =>
         default match {
           case Some(d) => d
@@ -75,7 +75,7 @@ object Question {
     if (posibleValues.nonEmpty) println(s"possible values: ${posibleValues.mkString(", ")}")
     default.foreach(x => println(s"Default value: $x"))
     print(s"$name > ")
-    (Console.readLine.split(",").toList.map(_.trim), default) match {
+    (scala.io.StdIn.readLine.split(",").toList.map(_.trim), default) match {
       case (List(""), Some(d)) => d
       case (List(""), None) =>
         println("ERROR: Value is required")

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala

@@ -523,16 +523,14 @@ class SummaryDbWrite(val db: Database)(implicit val ec: ExecutionContext) extend
 
   /** This method will create all tables */
   def createTables(): Unit = {
-    try {
-      val setup = DBIO.seq(
-        (runs.schema ++ samples.schema ++
-          libraries.schema ++ pipelines.schema ++
-          modules.schema ++ stats.schema ++ settings.schema ++
-          files.schema ++ executables.schema).create
-      )
-      val setupFuture = db.run(setup)
-      Await.result(setupFuture, Duration.Inf)
-    }
+    val setup = DBIO.seq(
+      (runs.schema ++ samples.schema ++
+        libraries.schema ++ pipelines.schema ++
+        modules.schema ++ stats.schema ++ settings.schema ++
+        files.schema ++ executables.schema).create
+    )
+    val setupFuture = db.run(setup)
+    Await.result(setupFuture, Duration.Inf)
   }
 
   /** This method will create a new run and return the runId */

tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/Tarmac.scala

@@ -68,14 +68,14 @@ class Tarmac(val parent: Configurable)
     )
   }
 
-  def init() = {}
+  def init(): Unit = {}
 
-  def biopetScript() = {
+  def biopetScript(): Unit = {
     addSamplesJobs()
     addSummaryJobs()
   }
 
-  def addMultiSampleJobs() = {
+  def addMultiSampleJobs(): Unit = {
     val initRefMap = samples map {
       case (sampleName, sample) => sample -> getReferenceSamplesForSample(sampleName)
     }
@@ -383,7 +383,7 @@ class Tarmac(val parent: Configurable)
    */
   def createXhmmReferenceJobs(sample: Sample,
                               referenceSamples: Set[Sample],
-                              outputDirectory: File): Tuple2[List[QFunction], File] = {
+                              outputDirectory: File): (List[QFunction], File) = {
     /* XHMM requires refset including self */
     val totalSet = referenceSamples + sample
     val merger = new XhmmMergeGatkDepths(this)
@@ -431,7 +431,7 @@ class Tarmac(val parent: Configurable)
     zscore
   }
 
-  def createXhmmZscore(sample: Sample, referenceMatrix: File): Tuple2[List[QFunction], File] = {
+  def createXhmmZscore(sample: Sample, referenceMatrix: File): (List[QFunction], File) = {
 
     // the filtered and centered matrix
     val filtMatrix = new XhmmMatrix(this)
@@ -494,7 +494,7 @@ class Tarmac(val parent: Configurable)
     protected lazy val outputXhmmCountJob: String \/ QFunction = {
       val outFile = new File(xhmmDir, s"$name.dcov")
       (inputXhmmCountFile, bamFile) match {
-        case (Some(f), _) => {
+        case (Some(f), _) =>
           if (bamFile.isDefined) {
             logger.warn(
               s"Both BAM and Xhmm count files are given for sample $name. The BAM file will be ignored")
@@ -503,11 +503,9 @@ class Tarmac(val parent: Configurable)
           ln.input = f
           ln.output = outFile
           \/-(ln)
-        }
-        case (None, Some(bam)) => {
+        case (None, Some(bam)) =>
           val dcov = DepthOfCoverage(root, List(bam), outFile, List(targets))
           \/-(dcov)
-        }
         case _ =>
           -\/(
             s"Cannot find bam file or xhmm count file for sample" +
@@ -522,6 +520,7 @@ class Tarmac(val parent: Configurable)
         case \/-(ln: Ln) => \/-(ln.output)
         case \/-(doc: DepthOfCoverage) => \/-(doc.intervalSummaryFile)
         case -\/(error) => -\/(error)
+        case _ => throw new IllegalStateException("This should not be reachable")
       }
     }
 
@@ -534,7 +533,7 @@ class Tarmac(val parent: Configurable)
     protected lazy val outputWisecondorCountJob: String \/ QFunction = {
       val outFile = new File(wisecondorDir, s"$name.wisecondor.bed")
       (inputWisecondorCountFile, bamFile) match {
-        case (Some(f), _) => {
+        case (Some(f), _) =>
           if (bamFile.isDefined) {
             logger.warn(
               s"Both BAM and Wisecondor count files are given for sample $name. The BAM file will be ignored")
@@ -543,14 +542,12 @@ class Tarmac(val parent: Configurable)
           ln.input = f
           ln.output = outFile
           \/-(ln)
-        }
-        case (None, Some(bam)) => {
+        case (None, Some(bam)) =>
           val counter = new WisecondorCount(root)
           counter.inputBam = bam
           counter.output = outFile
           counter.binFile = Some(targets)
           \/-(counter)
-        }
         case _ =>
           -\/(
             s"Cannot find bam file or wisecondor count for sample" +
@@ -565,6 +562,7 @@ class Tarmac(val parent: Configurable)
         case \/-(ln: Ln) => \/-(ln.output)
         case \/-(count: WisecondorCount) => \/-(count.output)
         case -\/(error) => -\/(error)
+        case _ => throw new IllegalStateException("This should not be reachable")
       }
     }
 
@@ -582,6 +580,7 @@ class Tarmac(val parent: Configurable)
       outputWisecondorGccJob match {
         case \/-(gcc: WisecondorGcCorrect) => \/-(gcc.output)
         case -\/(error) => -\/(error)
+        case _ => throw new IllegalStateException("This should not be reachable")
       }
     }