Adding Scaladocs to KrakenReportToJson and remove redundant code

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

@@ -18,9 +18,9 @@ package nl.lumc.sasc.biopet.extensions.kraken
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
 /** Extension for Kraken */
 class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Version {
@@ -65,13 +65,13 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Vers
 
   /** Returns command to execute */
   def cmdLine = required(executable) +
-    "--db" + required(db) +
+    required("--db", db) +
     optional("--threads", nCoresRequest) +
     conditional(quick, "--quick") +
     optional("--min_hits", minHits) +
     optional("--unclassified-out ", unclassified_out.get) +
     optional("--classified-out ", classified_out.get) +
-    "--output" + required(output) +
+    required("--output", output) +
     conditional(preLoad, "--preload") +
     conditional(paired, "--paired") +
     conditional(paired, "--check-names") +

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

@@ -9,7 +9,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
 
 /**
  * KrakenReportToJson function class for usage in Biopet pipelines
@@ -51,12 +51,5 @@ object KrakenReportToJson {
     report.output = new File(output, input.getName.substring(0, input.getName.lastIndexOf(".")) + ".kraken.json")
     report
   }
-
-  def apply(root: Configurable, input: File, outDir: String): KrakenReportToJson = {
-    val report = new KrakenReportToJson(root)
-    report.inputReport = input
-    report.output = new File(outDir, input.getName.substring(0, input.getName.lastIndexOf(".")) + ".kraken.json")
-    report
-  }
 }
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala

@@ -92,6 +92,15 @@ object KrakenReportToJson extends ToolCommand {
     .parse(args, Args())
     .getOrElse(sys.exit(1))
 
+  /**
+   * Takes a line from the kraken report, converts into Map with taxonID and
+   * information on this hit as `KrakenHit`. `KrakenHit` is used later on for
+   * building the tree
+   *
+   * @param krakenRawHit Line from the KrakenReport output
+   * @param skipNames Specify to skip names in the report output to reduce size of JSON
+   * @return
+   */
   def parseLine(krakenRawHit: String, skipNames: Boolean): Map[Long, KrakenHit] = {
     val values: Array[String] = krakenRawHit.stripLineEnd.split("\t")
 
@@ -118,6 +127,14 @@ object KrakenReportToJson extends ToolCommand {
       ))
   }
 
+  /**
+   * Read the `KrakenReport` output and transform into `Map` by TaxonID and `KrakenHit`
+   * A JSON-string output is given.
+   *
+   * @param reportRaw The `KrakenReport` output
+   * @param skipNames Specify to skip names in the report output to reduce size of JSON
+   * @return
+   */
   def reportToJson(reportRaw: File, skipNames: Boolean): String = {
     val reader = Source.fromFile(reportRaw)