Added scala docs

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

@@ -25,9 +25,7 @@ import scala.util.matching.Regex
 import java.io.FileInputStream
 import java.security.MessageDigest
 
-/**
- * Biopet command line trait to auto check executable and cluster values
- */
+/** Biopet command line trait to auto check executable and cluster values */
 trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
   analysisName = configName
 
@@ -47,14 +45,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
    */
   protected[core] def beforeCmd {}
 
-  /**
-   * Can override this method. This is executed after the script is done en queue starts to generate the graph
-   */
+  /** Can override this method. This is executed after the script is done en queue starts to generate the graph */
   protected[core] def beforeGraph {}
 
-  /**
-   * Set default output file, threads and vmem for current job
-   */
+  /** Set default output file, threads and vmem for current job */
   override def freezeFieldValues() {
     preProcesExecutable
     beforeGraph
@@ -118,9 +112,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
   }
 
-  /**
-   * executes checkExecutable method and fill job report
-   */
+  /** executes checkExecutable method and fill job report */
   final protected def preCmdInternal {
     preProcesExecutable
 
@@ -133,10 +125,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     addJobReportBinding("version", getVersion)
   }
 
-  /**
-   * Command to get version of executable
-   * @return
-   */
+  /** Command to get version of executable */
   protected def versionCommand: String = null
 
   /** Regex to get version from version command output */
@@ -205,9 +194,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   }
 }
 
-/**
- * stores global caches
- */
+/** stores global caches */
 object BiopetCommandLineFunctionTrait {
   import scala.collection.mutable.Map
   private val versionCache: Map[String, String] = Map()

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

@@ -21,6 +21,11 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
+/**
+ * Extension for bowtie 1
+ *
+ * Based on version 1.1.1
+ */
 class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Fastq file R1", shortName = "R1")
   var R1: File = null
@@ -53,6 +58,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   var strata: Boolean = config("strata", default = false)
   var maqerr: Option[Int] = config("maqerr")
 
+  /** return commandline to execute */
   def cmdLine = {
     required(executable) +
       optional("--threads", nCoresRequest) +

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

@@ -20,6 +20,9 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/**
+ * Extension for GNU cat
+ */
 class Cat(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input file", required = true)
   var input: List[File] = Nil
@@ -29,10 +32,22 @@ class Cat(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "cat")
 
+  /** return commandline to execute */
   def cmdLine = required(executable) + repeat(input) + " > " + required(output)
 }
 
+
+/**
+ * Object for constructors for cat
+ */
 object Cat {
+  /**
+   * Basis constructor
+   * @param root root object for config
+   * @param input list of files to use
+   * @param output output File
+   * @return
+   */
   def apply(root: Configurable, input: List[File], output: File): Cat = {
     val cat = new Cat(root)
     cat.input = input

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

@@ -24,6 +24,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import scala.collection.mutable
 import scala.io.Source
 
+/**
+ * Extension for cutadept
+ * Based on version 1.5
+ */
 class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
   @Input(doc = "Input fastq file")
   var fastq_input: File = _
@@ -39,17 +43,15 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
   override val versionRegex = """(.*)""".r
 
   var default_clip_mode: String = config("default_clip_mode", default = "3")
-  var opt_adapter: Set[String] = Set()
-  if (config.contains("adapter")) for (adapter <- config("adapter").asList) opt_adapter += adapter.toString
-  var opt_anywhere: Set[String] = Set()
-  if (config.contains("anywhere")) for (adapter <- config("anywhere").asList) opt_anywhere += adapter.toString
-  var opt_front: Set[String] = Set()
-  if (config.contains("front")) for (adapter <- config("front").asList) opt_front += adapter.toString
+  var opt_adapter: Set[String] = config("adapter", default = Nil)
+  var opt_anywhere: Set[String] = config("anywhere", default = Nil)
+  var opt_front: Set[String] = config("front", default = Nil)
 
   var opt_discard: Boolean = config("discard", default = false)
   var opt_minimum_length: Int = config("minimum_length", 1)
   var opt_maximum_length: Option[Int] = config("maximum_length")
 
+  /** return commandline to execute */
   def cmdLine = required(executable) +
     // options
     repeat("-a", opt_adapter) +
@@ -63,6 +65,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
     required("--output", fastq_output) +
     " > " + required(stats_output)
 
+  /** Output summary stats */
   def summaryStats: Map[String, Any] = {
     val trimR = """.*Trimmed reads: *(\d*) .*""".r
     val tooShortR = """.*Too short reads: *(\d*) .*""".r
@@ -89,6 +92,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
     )
   }
 
+  /** Merges values that can be merged for the summary */
   override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
     (v1, v2) match {
       case (v1: Int, v2: Int) => v1 + v2

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

@@ -22,6 +22,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 
+/**
+ * Extension for fastqc
+ * Based on version 0.10.1 and 0.11.2
+ */
 class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Contaminants", required = false)
@@ -48,6 +52,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   override def versionCommand = executable + " --version"
   override val defaultThreads = 4
 
+  /** Sets contaminants and adapters when not yet set */
   override def beforeGraph {
     this.preProcesExecutable
 
@@ -78,6 +83,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
     }
   }
 
+  /** return commandline to execute */
   def cmdLine = required(executable) +
     optional("--java", java_exe) +
     optional("--threads", threads) +

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

@@ -21,6 +21,9 @@ import org.broadinstitute.gatk.queue.function.InProcessFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import nl.lumc.sasc.biopet.core.config.Configurable
 
+/**
+ * This class can execute ln as InProcessFunction or used to only generate the ln command
+ */
 class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   this.analysisName = getClass.getSimpleName
 
@@ -35,12 +38,14 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
 
   var relative: Boolean = true
 
+  /** Generate out file for job */
   override def freezeFieldValues(): Unit = {
     val outLog: String = ".%s.%s.out".format(out.getName, analysisName)
     jobOutputFile = new File(out.getAbsoluteFile.getParentFile, outLog)
     super.freezeFieldValues()
   }
 
+  /** return commandline to execute */
   lazy val cmd: String = {
     lazy val inCanonical: String = {
       // need to remove "/~" to correctly expand path with tilde
@@ -113,7 +118,17 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   }
 }
 
+/** Object for constructors for ln */
 object Ln {
+  /**
+   * Basis constructor
+   * @param root root object for config
+   * @param input list of files to use
+   * @param output output File
+   * @param relative make reletive links (default true)
+   * @return
+   */
+
   def apply(root: Configurable, input: File, output: File, relative: Boolean = true): Ln = {
     val ln = new Ln(root)
     ln.in = input

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala

@@ -32,6 +32,7 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "md5sum")
 
+  /** return commandline to execute */
   def cmdLine = required(executable) + required(input) + " > " + required(output)
 
   def getSummary: Json = {
@@ -42,7 +43,9 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
   }
 }
 
+/** Object for constructors for md5sum */
 object Md5sum {
+  /** Makes md5sum with md5 file in given dir */
   def apply(root: Configurable, fastqfile: File, outDir: File): Md5sum = {
     val md5sum = new Md5sum(root)
     md5sum.input = fastqfile
@@ -50,6 +53,7 @@ object Md5sum {
     return md5sum
   }
 
+  /** Makes md5sum with md5 file in same dir as input file */
   def apply(root: Configurable, file: File): Md5sum = {
     val md5sum = new Md5sum(root)
     md5sum.input = file