Added more scala docs

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

@@ -17,16 +17,28 @@ package nl.lumc.sasc.biopet.core
 
 import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 
+/**
+ * Biopet commandline class for java based programs
+ */
 trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
-  executable = "java"
+  executable = config("java", default = "java", submodule = "java", freeVar = false)
 
   javaGCThreads = config("java_gc_threads")
   javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
   javaGCTimeLimit = config("java_gc_timelimit")
 
-  override def javaOpts = super.javaOpts + optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
+  /**
+   * Constructs java opts, this adds scala threads
+   * @return
+   */
+  override def javaOpts = super.javaOpts +
+    optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
 
+  /**
+   * Sets memory limit
+   */
   override def afterGraph {
+    super.afterGraph
     memoryLimit = config("memory_limit")
   }
 
@@ -38,7 +50,6 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
     preCmdInternal
     val cmd = super.commandLine
     val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
-    //    addJobReportBinding("command", cmd)
     return cmd
   }
 }

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

@@ -24,6 +24,9 @@ import org.broadinstitute.gatk.queue.function.QFunction
 import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 
+/**
+ * Base for biopet pipeline
+ */
 trait BiopetQScript extends Configurable with GatkLogging {
 
   @Argument(doc = "JSON config file(s)", fullName = "config_file", shortName = "config", required = false)
@@ -43,13 +46,21 @@ trait BiopetQScript extends Configurable with GatkLogging {
 
   var outputFiles: Map[String, File] = Map()
 
+  /** Get implemented from org.broadinstitute.gatk.queue.QScript */
   var qSettings: QSettings
 
+  /** Get implemented from org.broadinstitute.gatk.queue.QScript */
+  var functions: Seq[QFunction]
+
+  /** Init for pipeline */
   def init
-  def biopetScript
 
-  var functions: Seq[QFunction]
+  /** Pipeline itself */
+  def biopetScript
 
+  /**
+   * Script from queue itself, final to force some checks for each pipeline and write report
+   */
   final def script() {
     outputDir = config("output_dir", required = true)
     if (!outputDir.endsWith("/")) outputDir += "/"
@@ -68,10 +79,16 @@ trait BiopetQScript extends Configurable with GatkLogging {
     Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
   }
 
-  def add(functions: QFunction*) // Gets implemeted at org.broadinstitute.sting.queue.QScript
+  /** Get implemented from org.broadinstitute.gatk.queue.QScript */
+  def add(functions: QFunction*)
+
+  /**
+   * Function to set isIntermediate and add in 1 line
+   * @param function
+   * @param isIntermediate
+   */
   def add(function: QFunction, isIntermediate: Boolean = false) {
     function.isIntermediate = isIntermediate
     add(function)
   }
-
 }

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

@@ -15,6 +15,9 @@
  */
 package nl.lumc.sasc.biopet.core
 
+/**
+ * This trait is used in the biopet executable
+ */
 trait MainCommand {
 
   lazy val commandName = this.getClass.getSimpleName

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

@@ -20,10 +20,21 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
 
+/**
+ * Wrapper around executable from Queue
+ */
 trait PipelineCommand extends MainCommand with GatkLogging {
 
+  /**
+   * Gets location of compiled class of pipeline
+   * @return path from classPath to class file
+   */
   def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
 
+  /**
+   * Class can be used directly from java with -cp option
+   * @param args
+   */
   def main(args: Array[String]): Unit = {
     val argsSize = args.size
     for (t <- 0 until argsSize) {

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

@@ -15,10 +15,16 @@
  */
 package nl.lumc.sasc.biopet.core
 
+/**
+ * Trait for biopet tools, sets some default args
+ */
 trait ToolCommand extends MainCommand with Logging {
-  protected abstract class AbstractArgs {
-  }
+  /** Placeholder for args */
+  protected abstract class AbstractArgs { }
 
+  /**
+   * Abstract opt parser to add efault args to each biopet tool
+   */
   protected abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
     opt[String]('l', "log_level") foreach { x =>
       x.toLowerCase match {

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

@@ -39,14 +39,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
+/*
+ * This is a modifed version of org.broadinstitute.gatk.queue.QCommandLine, works without compiling a scala files but used build in class files to skip compile step
+ */
+
 package nl.lumc.sasc.biopet.core.workaround
 
 import java.io.File
 import org.broadinstitute.gatk.utils.commandline._
 import org.broadinstitute.gatk.queue.util._
-import org.broadinstitute.gatk.queue.QCommandPlugin
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.QScriptManager
+import org.broadinstitute.gatk.queue.{ QCommandPlugin, QScript, QScriptManager}
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
 import collection.JavaConversions._